diff --git a/releases/EDAM.obo b/releases/EDAM.obo
index 8941d42..0a6e748 100644
--- a/releases/EDAM.obo
+++ b/releases/EDAM.obo
@@ -1,16 +1,16 @@
 format-version: 1.2
-date: 18:08:2010 14:15
-data-version:  Beta08
+date: 07:10:2010 13:29
+data-version:  Beta09
 ! Use for mapping to "global" id space(s) e.g.: 
 ! idspace: EDAM urn:lsid:ebi.ac.uk:edam: "EDAM terms"
 ! idspace: EDAM http://purl.org/edam/ "EDAM terms"
-! NEXT term number is 2246
-subsetdef: EDAM_EXTRA "EDAM extra terms"
+! NEXT term number is 2330
 ! xref: WHATIF: CorrectedPDBasXML
 ! xref: http://www.geneontology.org/doc/GO.xrf_abbs: FB
 ! xref: Moby:GI_Gene
 ! xref: Moby_namespace:iHOPorganism
 ! xref: SO:0000348
+! xref: BioCatalogue:Protein Multiple Alignment
 
 
 
@@ -414,7 +414,7 @@ relationship: has_attribute EDAM:0000841 ! Undefined
 id: EDAM:0000021
 name: Amino acid
 namespace: entity
-def: "The building block of proteins, an alpha amino acid consists of a carbon atom (C-alpha) attached to a hydrogen atom, an amino group, a carboxylate group and and one of (typically) 20 common R-groups (side-chain)." [EDAM:EBI "EMBRACE definition"]
+def: "The building block of proteins, an alpha amino acid consists of a carbon atom (C-alpha) attached to a hydrogen atom, an amino group, a carboxylate group and one of (typically) 20 common R-groups (side-chain)." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000018 ! Biomonomer
 relationship: is_concern_of EDAM:0000076 ! Undefined
 relationship: has_identifier EDAM:0000994 ! Amino acid identifier
@@ -641,7 +641,7 @@ relationship: has_attribute EDAM:0001213 ! RNA sequence
 id: EDAM:0000036
 name: Peptide
 namespace: entity
-def: "An organic polymer of alpha amino acid residues in a short unbranched chain.  Peptides typically have fewer than 50 subunits and can be made synthetically." [EDAM:EBI "EMBRACE definition"]
+def: "An organic polymer of alpha amino acid residues in a short unbranched chain. Peptides typically have fewer than 50 subunits and can be made synthetically." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000025 ! Polypeptide
 relationship: is_concern_of EDAM:0000076 ! Undefined
 relationship: has_identifier EDAM:0000982 ! Molecule identifier
@@ -878,7 +878,7 @@ relationship: has_attribute EDAM:0000841 ! Undefined
 id: EDAM:0001854
 name: Binding site
 namespace: entity
-def: "A region of a molecular surface involved in interactions with other molecules" [EDAM:EBI "EMBRACE definition"]
+def: "A region of a molecular surface involved in interactions with other molecules." [EDAM:EBI "EMBRACE definition"]
 xref: SO:0000409
 is_a: EDAM:0000010 ! Entity feature
 relationship: is_concern_of EDAM:0000076 ! Undefined
@@ -1116,7 +1116,7 @@ relationship: has_attribute EDAM:0000841 ! Undefined
 id: EDAM:0000065
 name: Protein domain
 namespace: entity
-def: "A region of a protein (typically a region of a single polypeptide chain) forming a distinct, compact conformation.  Domains show some independence in terms of evolution, folding, structure or function and (typically) reoccur in other proteins." [EDAM:EBI "EMBRACE definition"]
+def: "A region of a protein (typically a region of a single polypeptide chain) forming a distinct, compact conformation. Domains show some independence in terms of evolution, folding, structure or function and (typically) reoccur in other proteins." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000049 ! Protein feature
 relationship: is_concern_of EDAM:0000076 ! Undefined
 relationship: has_identifier EDAM:0000841 ! Undefined
@@ -1191,7 +1191,7 @@ relationship: has_attribute EDAM:0000841 ! Undefined
 id: EDAM:0000067
 name: Proteome
 namespace: entity
-def: "An organisms total complement of expressed proteins.  More specifically, those proteins expressed in a cell, tissue or the whole organism under defined conditions at a specific time." [EDAM:EBI "EMBRACE definition"]
+def: "An organisms total complement of expressed proteins. More specifically, those proteins expressed in a cell, tissue or the whole organism under defined conditions at a specific time." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000011 ! Entity collection
 relationship: is_concern_of EDAM:0000076 ! Undefined
 relationship: has_identifier EDAM:0000842 ! Identifier
@@ -1329,7 +1329,7 @@ relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
 id: EDAM:0000077
-name: Nucleic acid analysis
+name: Nucleic acids
 namespace: topic
 def: "Nucleic acid data and analysis." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000003 ! Topic
@@ -1337,7 +1337,7 @@ relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
 id: EDAM:0000078
-name: Protein analysis
+name: Proteins
 namespace: topic
 def:  "Protein data and analysis." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000003 ! Topic
@@ -1345,7 +1345,7 @@ relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
 id: EDAM:0000079
-name: Metabolite analysis
+name: Metabolites
 namespace: topic
 def: "Metabolite data and analysis." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000003 ! Topic
@@ -1357,6 +1357,7 @@ name: Sequence analysis
 namespace: topic
 def: "Analyse molecular sequences." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000003 ! Topic
+xref: BioCatalogue:Sequence Analysis
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
@@ -1379,7 +1380,7 @@ relationship: concerns EDAM:0000008 ! Undefined
 id: EDAM:0000083
 name: Alignment
 namespace: topic
-def: "Generation or analysis of alignments of molecular sequences, structures or profiles (representing a sequence or structure alignment)." [EDAM:EBI "EMBRACE definition"]
+def: "Generate or analyse alignments of molecular sequences, structures or profiles (representing a sequence or structure alignment)." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000003 ! Topic
 relationship: concerns EDAM:0000008 ! Undefined
 
@@ -1389,17 +1390,64 @@ name: Phylogenetics
 namespace: topic
 def: "Study evolutionary relationships amongst organisms and the genetic basis of heredity and variation." [EDAM:EBI "EMBRACE definition"]
 comment: Phylogenetics involves phylogenetic tree construction, manipulation, visualisation and analysis.
+xref: BioCatalogue:Phylogeny
+xref: BioCatalogue:Statistical Robustness
 is_a: EDAM:0000003 ! Topic
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
+id: EDAM:0000200
+name: Microarrays
+namespace: topic
+def: "Process, analyse, interpret and visualise microarray data or design probes and experiments." [EDAM:EBI "EMBRACE definition"]
+xref: BioCatalogue:Microarrays
+is_a: EDAM:0000003 ! Topic
+relationship: concerns EDAM:0000008 ! Undefined
+
+[Term]
+id: EDAM:0000121
+name: Proteomics
+namespace: topic
+def: "Study whole proteomes of organisms." [EDAM:EBI "EMBRACE definition"]
+comment: Proteomics uses high-throughput methods to separate, characterize and identify expressed proteins or analyse protein expression data (for example in different cells or tissues).
+synonym: "Protein expression" EXACT []
+xref: BioCatalogue:Proteomics
+is_a: EDAM:0000003 ! Topic
+! is_a: EDAM:0000078 ! Proteins
+relationship: concerns EDAM:0000008 ! Undefined
+
+
+[Term]
+id: EDAM:0000093
+name: Genomics
+namespace: topic
+def: "Study whole genomes of organisms." [EDAM:EBI "EMBRACE definition"]
+xref: BioCatalogue:Genomics
+is_a: EDAM:0000003 ! Topic
+relationship: concerns EDAM:0000008 ! Undefined
+
+
+[Term]
 id: EDAM:0000085
 name: Functional genomics
 namespace: topic
 def: "Study gene or protein functions and their interactions." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000003 ! Topic
+xref: BioCatalogue:Functional Genomics
+is_a: EDAM:0000093 ! Genomics
+relationship: concerns EDAM:0000008 ! Undefined
+
+[Term]
+id: EDAM:0000122
+name: Structural genomics
+namespace: topic
+def: "Determine or study the three dimensional structure for all (available) proteins in a given organism." [EDAM:EBI "EMBRACE definition"]
+comment: Structural genomics uses experimental data (for example from X-ray crystallography or NMR spectroscopy) and computational methods (for example molecular modelling).
+xref: BioCatalogue:Structural Genomics
+is_a: EDAM:0000093 ! Genomics
+! is_a: EDAM:0000078 ! Proteins
 relationship: concerns EDAM:0000008 ! Undefined
 
+
 [Term]
 id: EDAM:0000086
 name: Model organisms
@@ -1420,7 +1468,7 @@ relationship: concerns EDAM:0000008 ! Undefined
 id: EDAM:0000088
 name: Literature and documentation
 namespace: topic
-def: "Study biomedical and informatic literature, bibliographic data and documentation." [EDAM:EBI "EMBRACE definition"]
+def: "Biomedical and informatic literature, bibliographic data and documentation." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000003 ! Topic
 relationship: concerns EDAM:0000008 ! Undefined
 
@@ -1428,7 +1476,8 @@ relationship: concerns EDAM:0000008 ! Undefined
 id: EDAM:0000089
 name: Ontologies
 namespace: topic
-def: "Study biomedical ontologies, controlled vocabularies, glossaries etc." [EDAM:EBI "EMBRACE definition"]
+def: "Biomedical ontologies, controlled vocabularies, glossaries etc." [EDAM:EBI "EMBRACE definition"]
+xref: BioCatalogue:Ontology
 is_a: EDAM:0000003 ! Topic
 relationship: concerns EDAM:0000008 ! Undefined
 
@@ -1437,6 +1486,17 @@ id: EDAM:0000090
 name: Database search and retrieval
 namespace: topic
 def: "Search or query a biological database or ontology and retrieve entries or other information." [EDAM:EBI "EMBRACE definition"]
+xref: BioCatalogue:Data Retrieval
+xref: BioCatalogue:Identifier Retrieval
+xref: BioCatalogue:Image Retrieval
+is_a: EDAM:0000003 ! Topic
+relationship: concerns EDAM:0000008 ! Undefined
+
+[Term]
+id: EDAM:0000219
+name: Annotation
+namespace: topic
+def: "Annotate biological database or ontology entities." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000003 ! Topic
 relationship: concerns EDAM:0000008 ! Undefined
 
@@ -1444,7 +1504,7 @@ relationship: concerns EDAM:0000008 ! Undefined
 id: EDAM:0000091
 name: Database and file management
 namespace: topic
-def: "Manage a biological database or file, for example indexing, annotation, reformatting etc." [EDAM:EBI "EMBRACE definition"]
+def: "Manage a biological database or file, for example submissions, indexing, reformatting etc." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000003 ! Topic
 relationship: concerns EDAM:0000008 ! Undefined
 
@@ -1456,47 +1516,76 @@ def: "Render (display or print) molecular sequences, structures or other biomole
 is_a: EDAM:0000003 ! Topic
 relationship: concerns EDAM:0000008 ! Undefined
 
+[Term]
+id: EDAM:0002282
+name: Datatypes, workflows and data handling
+namespace: topic
+def: "Handling of biological data in a generic sense, including datatypes, data identifiers, data management, workflows etc." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0000003 ! Topic
+relationship: concerns EDAM:0000008 ! Undefined
 
+[Term]
+id: EDAM:0002258
+name: Chemoinformatics
+namespace: topic
+def: "Computing of data-centric problems in chemistry." [EDAM:EBI "EMBRACE definition"]
+synonym: "Cheminformatics" EXACT []
+synonym: "Chemical informatics" EXACT []
+xref: BioCatalogue:Chemoinformatics
+is_a: EDAM:0000003 ! Topic
+relationship: concerns EDAM:0000008 ! Undefined
 
+[Term]
+id: EDAM:0002259
+name: Systems biology and modelling
+namespace: topic
+def: "Holistic analysis of biological systems and modelling of the systems and interactions therein." [EDAM:EBI "EMBRACE definition"]
+xref: BioCatalogue:Systems Biology
+is_a: EDAM:0000003 ! Topic
+relationship: concerns EDAM:0000008 ! Undefined
 
-
+[Term]
+id: EDAM:0002269
+name: Biostatistics 
+namespace: topic
+def: "Apply statistical methods to biological problems." [EDAM:EBI "EMBRACE definition"]
+synonym: "Biometry" EXACT []
+synonym: "Biometrics" EXACT []
+xref: BioCatalogue:Biostatistics
+is_a: EDAM:0000003 ! Topic
+relationship: concerns EDAM:0000008 ! Undefined
 
 
 
 
 !
-! Topic<-Nucleic acid analysis
+! Topic<-Nucleic acids
 !
 [Term]
-id: EDAM:0000093
-name: Genomics
-namespace: topic
-def: "Study whole genomes of organisms." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000077 ! Nucleic acid analysis
-relationship: concerns EDAM:0000008 ! Undefined
-
-[Term]
 id: EDAM:0000094
-name: Nucleic acid physicochemical properties
+name: Nucleic acid physicochemistry
 namespace: topic
 def: "Determine, predict or analyse the physicochemical properties of a nucleic acid." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000077 ! Nucleic acid analysis
+is_a: EDAM:0000077 ! Nucleic acids
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
 id: EDAM:0000095
 name: Nucleic acid features
 namespace: topic
-def: "Identify, predict or analyse features of nucleic acid sequences and structures." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000077 ! Nucleic acid analysis
+def: "Identify, predict or analyse features of nucleic acid sequences." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0000160 ! Sequence features
+is_a: EDAM:0000096 ! Nucleic acid sequence analysis
 relationship: concerns EDAM:0000008 ! Undefined
 
+
 [Term]
 id: EDAM:0000096
 name: Nucleic acid sequence analysis
 namespace: topic
 def: "Nucleic acid sequence data and analysis." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000077 ! Nucleic acid analysis
+xref: BioCatalogue:Nucleotide Sequence Analysis
+is_a: EDAM:0000077 ! Nucleic acids
 is_a: EDAM:0000080 ! Sequence analysis
 relationship: concerns EDAM:0000008 ! Undefined
 
@@ -1504,72 +1593,44 @@ relationship: concerns EDAM:0000008 ! Undefined
 id: EDAM:0000097
 name: Nucleic acid structure analysis
 namespace: topic
-def: "Nucleic acid structural data and analysis." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000077 ! Nucleic acid analysis
+def: "Identify, predict, analyse or handle nucleic acid structure or structural features." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0000077 ! Nucleic acids
 is_a: EDAM:0000081 ! Structure analysis
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
 id: EDAM:0000098
-name: DNA analysis
+name: DNA
 namespace: topic
 def: "DNA data and analysis." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000077 ! Nucleic acid analysis
+is_a: EDAM:0000077 ! Nucleic acids
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
 id: EDAM:0000099
-name: RNA analysis
+name: RNA
 namespace: topic
 def: "RNA data and analysis." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000077 ! Nucleic acid analysis
+is_a: EDAM:0000077 ! Nucleic acids
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
 id: EDAM:0000100
 name: Nucleic acid restriction
 namespace: topic
-def: "Data and analysis concerning restriction enzymes, for example, predict, analyse or process restriction enzyme cleavage sites (restriction sites) in (typically) DNA sequences." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000077 ! Nucleic acid analysis
-relationship: concerns EDAM:0000008 ! Undefined
-
-
-
-!
-! Topic<-Nucleic acid analysis<-Genomics
-!
-[Term]
-id: EDAM:0000101
-name: Comparative genomics
-namespace: topic
-def: "Compare the structure or function of multiple genomes." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000093 ! Genomics
+def: "Study restriction enzymes and their cleavage sites, for example, identify restriction sites in DNA sequences." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0000096 ! Nucleic acid sequence analysis
+is_a: EDAM:0000132 ! Enzymes
 relationship: concerns EDAM:0000008 ! Undefined
 
-[Term]
-id: EDAM:0000102
-name: Sequencing
-namespace: topic
-def: "Determine complete nucleotide sequences from sequencing project data." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000093 ! Genomics
-relationship: concerns EDAM:0000008 ! Undefined
 
-[Term]
-id: EDAM:0000103
-name: Genetic mapping
-namespace: topic
-def: "Identify or map genetic markers in DNA sequences, for example to determine a genetic (linkage) map for a chromosome, or analyse known genetic maps." [EDAM:EBI "EMBRACE definition"]
-synonym: "Genetic linkage" EXACT []
-synonym: "Linkage mapping" EXACT []
-is_a: EDAM:0000093 ! Genomics
-relationship: concerns EDAM:0000008 ! Undefined
 
 
 
 
 
 !
-! Topic<-Nucleic acid analysis<-Nucleic acid physicochemical properties
+! Topic<-Nucleic acids<-Nucleic acid physicochemistry
 !
 
 [Term]
@@ -1578,36 +1639,39 @@ name: Nucleic acid denaturation
 namespace: topic
 def: "Analyse DNA or DNA/RNA denaturation (melting) including thermal and conformational properties." [EDAM:EBI "EMBRACE definition"]
 synonym: "DNA melting" EXACT []
-is_a: EDAM:0000094 ! Nucleic acid physicochemical properties
+is_a: EDAM:0000094 ! Nucleic acid physicochemistry
 relationship: concerns EDAM:0000008 ! Undefined
 
 
 
 
 !
-! Topic<-Nucleic acid analysis<-Nucleic acid features
+! Topic<-Nucleic acids<-Nucleic acid features
 !
 [Term]
 id: EDAM:0000105
 name: Nucleic acid sequence features
 namespace: topic
 def: "Identify, predict or analyse features in nucleic acid sequences." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000095 ! Nucleic acid features
-is_a: EDAM:0000160 ! Sequence features
-relationship: concerns EDAM:0000008 ! Undefined
+is_obsolete: true
+consider: EDAM:0000095 ! Nucleic acid features
+
 
 [Term]
 id: EDAM:0000106
 name: Nucleic acid structural features
 namespace: topic
 def: "Identify, predict or analyse nucleic acid structural features." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000077 ! Nucleic acid analysis
-is_a: EDAM:0000170 ! Structural features
+is_obsolete: true
+consider: EDAM:0000097 ! Nucleic acid structure analysis
+! is_a: EDAM:0000095 ! Nucleic acid features
+! is_a: EDAM:0000170 ! Structural features and motifs
+! is_a: EDAM:0000097 ! Nucleic acid structure analysis
 relationship: concerns EDAM:0000008 ! Undefined
 
 
 !
-! Topic<-Nucleic acid analysis<-Nucleic acid sequence analysis
+! Topic<-Nucleic acids<-Nucleic acid sequence analysis
 !
 [Term]
 id: EDAM:0000107
@@ -1624,6 +1688,7 @@ namespace: topic
 def: "Handle transcription and translation of nucleotide sequences." [EDAM:EBI "EMBRACE definition"]
 comment: For example, translate a nucleotide sequence or back translate a protein sequence, construct mRNA sequences from genomic sequences etc.
 is_a: EDAM:0000096 ! Nucleic acid sequence analysis
+is_a: EDAM:0000197 ! Gene expression
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
@@ -1633,6 +1698,7 @@ namespace: topic
 def: "Identify, predict, model or analyse genes or gene structure (promoters, coding regions, splice sites, etc) in DNA sequences." [EDAM:EBI "EMBRACE definition"]
 comment: Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc.
 synonym: "Gene prediction" EXACT []
+xref: BioCatalogue:Gene Prediction
 is_a: EDAM:0000096 ! Nucleic acid sequence analysis
 relationship: concerns EDAM:0000008 ! Undefined
 
@@ -1640,29 +1706,31 @@ relationship: concerns EDAM:0000008 ! Undefined
 
 
 !
-! Topic<-Nucleic acid analysis<-Nucleic acid sequence analysis<-Codon usage
+! Topic<-Nucleic acids<-Nucleic acid sequence analysis<-Codon usage
 !
 
 !
-! Topic<-Nucleic acid analysis<-Nucleic acid sequence analysis<-Transcription and translation
+! Topic<-Nucleic acids<-Nucleic acid sequence analysis<-Transcription and translation
 !
 
 
 !
-! Topic<-Nucleic acid analysis<-Nucleic acid sequence analysis<-Gene finding
+! Topic<-Nucleic acids<-Nucleic acid sequence analysis<-Gene finding
 !
 [Term]
 id: EDAM:0000110
-name: Transcription regulatory sequence analysis
+name: Transcription regulators
 namespace: topic
 def: "Identify, predict or analyse transcription regulatory motifs, patterns, elements or regions in DNA sequences." [EDAM:EBI "EMBRACE definition"]
-comment: This includes promoters, enhancers, silencers and boundary elements / insulators.  Transcription regulatory regions bind regulatory proteins such as transcription factors.
+comment: This includes promoters, enhancers, silencers and boundary elements / insulators. Transcription regulatory regions bind regulatory proteins such as transcription factors.
+xref: BioCatalogue:Transcription Factors
+is_a: EDAM:0000197 ! Gene expression
 is_a: EDAM:0000109 ! Gene finding
 relationship: concerns EDAM:0000008 ! Undefined
 
 
 !
-! Topic<-Nucleic acid analysis<-Nucleic acid sequence analysis<-Gene finding<-Transcription regulatory sequence analysis
+! Topic<-Nucleic acids<-Nucleic acid sequence analysis<-Gene finding<-Transcription regulators
 !
 
 [Term]
@@ -1670,7 +1738,8 @@ id: EDAM:0000111
 name: Promoters
 namespace: topic
 def: "Analyse, compare, classify or model promoters in DNA sequences." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000110 ! Transcription regulatory sequence analysis
+xref: BioCatalogue:Promoter Prediction
+is_a: EDAM:0000110 ! Transcription regulators
 relationship: concerns EDAM:0000008 ! Undefined
 
 
@@ -1682,7 +1751,7 @@ relationship: concerns EDAM:0000008 ! Undefined
 
 
 !
-! Topic<-Nucleic acid analysis<-Nucleic acid structure analysis
+! Topic<-Nucleic acids<-Nucleic acid structure analysis
 !
 [Term]
 id: EDAM:0000112
@@ -1695,19 +1764,19 @@ relationship: concerns EDAM:0000008 ! Undefined
 
 
 !
-! Topic<-Nucleic acid analysis<-DNA analysis
+! Topic<-Nucleic acids<-DNA
 !
 
 !
-! Topic<-Nucleic acid analysis<-RNA analysis
+! Topic<-Nucleic acids<-RNA
 !
 
 [Term]
 id: EDAM:0000113
-name: Functional RNA analysis
+name: Functional RNA
 namespace: topic
 def: "Analyse functional or non-coding RNA." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000099 ! RNA analysis
+is_a: EDAM:0000099 ! RNA
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
@@ -1715,7 +1784,7 @@ id: EDAM:0000114
 name: RNA splicing
 namespace: topic
 def: "Analyse RNA splicing, identify splice sites, calculate splicing alternatives etc." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000099 ! RNA analysis
+is_a: EDAM:0000099 ! RNA
 is_a: EDAM:0000197 ! Gene expression
 is_a: EDAM:0000096 ! Nucleic acid sequence analysis
 relationship: concerns EDAM:0000008 ! Undefined
@@ -1723,62 +1792,62 @@ relationship: concerns EDAM:0000008 ! Undefined
 
 
 !
-! Topic<-Nucleic acid analysis<-RNA analysis<-Functional RNA analysis
+! Topic<-Nucleic acids<-RNA<-Functional RNA
 !
 
 [Term]
 id: EDAM:0000115
-name: tRNA analysis
+name: tRNA
 namespace: topic
 def: "Transfer RNA (tRNA) data and analysis." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000113 ! Functional RNA analysis
+is_a: EDAM:0000113 ! Functional RNA
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
 id: EDAM:0000116
-name: rRNA analysis
+name: rRNA
 namespace: topic
 def: "Ribosomal RNA (rRNA) data and analysis." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000113 ! Functional RNA analysis
+is_a: EDAM:0000113 ! Functional RNA
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
 id: EDAM:0000117
-name: microRNA analysis
+name: microRNA
 namespace: topic
 def: "MicroRNA (miRNA) data and analysis." [EDAM:EBI "EMBRACE definition"]
 comment: Micro RNAs are short single stranded RNA molecules that regulate gene expression.
-is_a: EDAM:0000113 ! Functional RNA analysis
+is_a: EDAM:0000113 ! Functional RNA
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
 id: EDAM:0000118
-name: siRNA analysis
+name: siRNA
 namespace: topic
 def: "Small interfering (silencing) RNA (siRNA) data and analysis." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000113 ! Functional RNA analysis
+is_a: EDAM:0000113 ! Functional RNA
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
 id: EDAM:0000119
-name: piRNA analysis
+name: piRNA
 namespace: topic
 def: "Piwi-interacting RNA (piRNA) data and analysis." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000113 ! Functional RNA analysis
+is_a: EDAM:0000113 ! Functional RNA
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
 id: EDAM:0000120
-name: snoRNA analysis
+name: snoRNA
 namespace: topic
 def: "Small nucleolar RNA (snoRNAs) data and analysis." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000113 ! Functional RNA analysis
+is_a: EDAM:0000113 ! Functional RNA
 relationship: concerns EDAM:0000008 ! Undefined
 
 
 
 !
-! Topic<-Nucleic acid analysis<-Nucleic acid restriction
+! Topic<-Nucleic acids<-Nucleic acid restriction
 !
 
 
@@ -1791,43 +1860,24 @@ relationship: concerns EDAM:0000008 ! Undefined
 
 
 !
-! Topic<-Protein analysis
+! Topic<-Proteins
 !
-[Term]
-id: EDAM:0000121
-name: Proteomics
-namespace: topic
-def: "Study whole proteomes of organisms." [EDAM:EBI "EMBRACE definition"]
-comment: Proteomics uses high-throughput methods to separate, characterize and identify expressed proteins or analyse protein expression data (for example in different cells or tissues).
-synonym: "Protein expression" EXACT []
-is_a: EDAM:0000078 ! Protein analysis
-is_a: EDAM:0000085 ! Functional genomics
-relationship: concerns EDAM:0000008 ! Undefined
-
-[Term]
-id: EDAM:0000122
-name: Structural genomics
-namespace: topic
-def: "Determine the three dimensional structure for all proteins in a given organism." [EDAM:EBI "EMBRACE definition"]
-comment: Structural genomics uses experimental data (for example from X-ray crystallography or NMR spectroscopy) and computational methods (for example molecular modelling).
-is_a: EDAM:0000078 ! Protein analysis
-relationship: concerns EDAM:0000008 ! Undefined
-
 
 [Term]
 id: EDAM:0000123
-name: Protein physicochemical properties
+name: Protein physicochemistry
 namespace: topic
 def: "Determine, predict or analyse the physicochemical properties of peptides and proteins." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000078 ! Protein analysis
+is_a: EDAM:0000078 ! Proteins
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
 id: EDAM:0000124
 name: Protein features
 namespace: topic
-def: "Predict, identify or analyse features of protein sequences and structures." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000078 ! Protein analysis
+def: "Predict, identify or analyse features of protein sequences." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0000160 ! Sequence features
+is_a: EDAM:0000125 ! Protein sequence analysis
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
@@ -1835,8 +1885,9 @@ id: EDAM:0000125
 name: Protein sequence analysis
 namespace: topic
 def: "Protein sequence data and analysis." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000078 ! Protein analysis
+is_a: EDAM:0000078 ! Proteins
 is_a: EDAM:0000080 ! Sequence analysis
+xref: BioCatalogue:Protein Sequence Analysis
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
@@ -1844,16 +1895,17 @@ id: EDAM:0000126
 name: Protein structure analysis
 namespace: topic
 def: "Protein structural data and analysis." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000078 ! Protein analysis
+is_a: EDAM:0000078 ! Proteins
 is_a: EDAM:0000081 ! Structure analysis
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
 id: EDAM:0001775
-name: Protein function analysis
+name: Protein function
 namespace: topic
 def: "Protein functional data and analysis." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000078 ! Protein analysis
+xref: BioCatalogue:Function Prediction
+is_a: EDAM:0000078 ! Proteins
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
@@ -1861,15 +1913,18 @@ id: EDAM:0000127
 name: Protein domains
 namespace: topic
 def: "Protein structural domain data and analysis." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000078 ! Protein analysis
+xref: BioCatalogue:Domains
+is_a: EDAM:0002125 ! Protein tertiary structure analysis
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
 id: EDAM:0000128
 name: Protein interactions
 namespace: topic
-def: "Analyse protein-protein, protein-DNA/RNA and protein-ligand interactions." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000078 ! Protein analysis
+def: "Study protein-protein, protein-DNA/RNA and protein-ligand interactions." [EDAM:EBI "EMBRACE definition"]
+xref: BioCatalogue:Protein Interaction
+is_a: EDAM:0000078 ! Proteins
+is_a: EDAM:0000085 ! Functional genomics
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
@@ -1877,31 +1932,31 @@ id: EDAM:0000129
 name: Protein classification
 namespace: topic
 def: "Protein sequence or structure classification." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000078 ! Protein analysis
+is_a: EDAM:0000078 ! Proteins
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
 id: EDAM:0000130
 name: Protein folding, stability and design
 namespace: topic
-def: "Analyse or predict sequence-structure-function relationships, protein folding, the effect of mutation, protein design etc." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000078 ! Protein analysis
+def: "Analyse or predict sequence-structure-function relationships, protein folding, the effect of mutation and the implications for protein design." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0000078 ! Proteins
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
 id: EDAM:0000131
-name: Transmembrane protein analysis
+name: Transmembrane proteins
 namespace: topic
-def: "Data and analysis on transmembrane proteins / regions." [EDAM:EBI  "EMBRACE definition"]
-is_a: EDAM:0000078 ! Protein analysis
+def: "Handle or analyse transmembrane proteins / regions." [EDAM:EBI  "EMBRACE definition"]
+is_a: EDAM:0000078 ! Proteins
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
 id: EDAM:0002232
-name: Lipoprotein analysis
+name: Lipoproteins
 namespace: topic
-def: "Data and analysis on lipoproteins." [EDAM:EBI  "EMBRACE definition"]
-is_a: EDAM:0000078 ! Protein analysis
+def: "Handle or analyse lipoproteins." [EDAM:EBI  "EMBRACE definition"]
+is_a: EDAM:0000078 ! Proteins
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
@@ -1909,92 +1964,54 @@ id: EDAM:0000132
 name: Enzymes
 namespace: topic
 def: "Enzymes and the kinetics of enzyme-catalysed reactions." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000078 ! Protein analysis
-relationship: concerns EDAM:0000008 ! Undefined
-
-!
-! Topic<-Protein analysis<-Proteomics
-!
-[Term]
-id: EDAM:0000133
-name: Two-dimensional gel electrophoresis
-namespace: topic
-def: "Handle two-dimensional gel electrophoresis data." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000121 ! Proteomics
+is_a: EDAM:0000078 ! Proteins
 relationship: concerns EDAM:0000008 ! Undefined
 
 
-[Term]
-id: EDAM:0000134
-name: Mass spectrometry
-namespace: topic
-def: "Handle mass spectrometry and related data." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000121 ! Proteomics
-relationship: concerns EDAM:0000008 ! Undefined
 
-[Term]
-id: EDAM:0000135
-name: Protein microarrays
-namespace: topic
-def: "Protein microarray data and analysis." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000121 ! Proteomics
-is_a: EDAM:0000200 ! Microarrays
-is_a: EDAM:0000197 ! Gene expression
-relationship: concerns EDAM:0000008 ! Undefined
 
-!
-! Topic<-Protein analysis<-Structural genomics
-!
-[Term]
-id: EDAM:0000136
-name: X-ray crystallographic data analysis
-namespace: topic
-def: "Assign, validate or refine a protein structure from X-ray crystallography data." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000122 ! Structural genomics
-is_a: EDAM:0000126 ! Protein structure analysis
-relationship: concerns EDAM:0000008 ! Undefined
 
 
 
 !
-! Topic<-Protein analysis<-Protein physicochemical properties
+! Topic<-Proteins<-Protein physicochemistry
 !
 [Term]
 id: EDAM:0000137
 name: Protein hydropathy
 namespace: topic
 def: "Analyse the hydrophobic, hydrophilic and charge properties of a protein sequence or structure." [EDAM:EBI  "EMBRACE definition"]
-is_a: EDAM:0000123 ! Protein physicochemical properties
+is_a: EDAM:0000123 ! Protein physicochemistry
 relationship: concerns EDAM:0000008 ! Undefined
 
 
 !
-! Topic<-Protein analysis<-Protein features
+! Topic<-Proteins<-Protein features
 !
 [Term]
 id: EDAM:0000138
 name: Protein sequence features
 namespace: topic
 def: "Predict, identify or analyse features in protein sequences." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000124 ! Protein features
-is_a: EDAM:0000160 ! Sequence features
-is_a: EDAM:0000125 ! Protein sequence analysis
-relationship: concerns EDAM:0000008 ! Undefined
+is_obsolete: true
+consider: EDAM:0000124 ! Protein features
+
+
+
+
 
 [Term]
 id: EDAM:0000139
 name: Protein structural features
 namespace: topic
 def: "Predict, identify or analyse protein structural features." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000124 ! Protein features
-is_a: EDAM:0000170 ! Structural features
-is_a: EDAM:0000126 ! Protein structure analysis
-relationship: concerns EDAM:0000008 ! Undefined
+is_obsolete: true
+consider: EDAM:0000166 ! Protein structural motifs
 
 
 
 !
-! Topic<-Protein analysis<-Protein sequence analysis
+! Topic<-Proteins<-Protein sequence analysis
 !
 [Term]
 id: EDAM:0000140
@@ -2024,15 +2041,14 @@ relationship: concerns EDAM:0000008 ! Undefined
 
 
 !
-! Topic<-Protein analysis<-Protein structure analysis
+! Topic<-Proteins<-Protein structure analysis
 !
 [Term]
 id: EDAM:0002124
 name: Protein secondary structure analysis
 namespace: topic
 def: "Protein secondary structural data and analysis." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000078 ! Protein analysis
-is_a: EDAM:0000081 ! Structure analysis
+is_a: EDAM:0000126 ! Protein structure analysis
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
@@ -2040,8 +2056,7 @@ id: EDAM:0002125
 name: Protein tertiary structure analysis
 namespace: topic
 def: "Protein tertiary structural data and analysis." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000078 ! Protein analysis
-is_a: EDAM:0000081 ! Structure analysis
+is_a: EDAM:0000126 ! Protein structure analysis
 relationship: concerns EDAM:0000008 ! Undefined
 
 
@@ -2050,8 +2065,18 @@ id: EDAM:0000143
 name: Protein structure comparison
 namespace: topic
 def: "Compare two or more protein structures." [EDAM:EBI "EMBRACE definition"]
-comment: For example to identify structural neighbors, find structural similarities or define a structural core.
-is_a: EDAM:0000126 ! Protein structure analysis
+comment: Use this term for methods that are exclusively for protein structure. Methods might identify structural neighbors, find structural similarities or define a structural core.
+is_a: EDAM:0002125 ! Protein tertiary structure analysis
+is_a: EDAM:0001770 ! Structure comparison
+relationship: concerns EDAM:0000008 ! Undefined
+
+[Term]
+id: EDAM:0002280
+name: Nucleic acid structure comparison
+namespace: topic
+def: "Compare two or more nucleic acid (typically RNA) secondary or tertiary structures." [EDAM:EBI "EMBRACE definition"]
+comment: Use this term for methods that are exclusively for nucleic acid structures.
+is_a: EDAM:0000097 ! Nucleic acid structure analysis
 is_a: EDAM:0001770 ! Structure comparison
 relationship: concerns EDAM:0000008 ! Undefined
 
@@ -2060,8 +2085,8 @@ relationship: concerns EDAM:0000008 ! Undefined
 id: EDAM:0000144
 name: Protein residue interactions
 namespace: topic
-def: "Data and analysis on inter-atomic or inter-residue interactions in protein structures." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000126 ! Protein structure analysis
+def: "Analyse inter-atomic or inter-residue interactions in protein structures." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0002124 ! Protein secondary structure analysis
 relationship: concerns EDAM:0000008 ! Undefined
 
 
@@ -2070,28 +2095,40 @@ id: EDAM:0000145
 name: Protein flexibility and motion
 namespace: topic
 def: "Study flexibility and motion in protein structure." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000126 ! Protein structure analysis
+is_a: EDAM:0002125 ! Protein tertiary structure analysis
+is_a: EDAM:0000176 ! Molecular dynamics
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
 id: EDAM:0000146
-name: Protein surface analysis
+name: Protein surfaces
 namespace: topic
-def: "Analyse or visualise the surface (shape, hydropathy, electrostatic patches etc) of a protein structure, including biological interfaces with other molecules." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000126 ! Protein structure analysis
+def: "Caclulate, analyse or visualise the surface (shape, hydropathy, electrostatic patches etc) of a protein structure, including biological interfaces with other molecules." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0002125 ! Protein tertiary structure analysis
 relationship: concerns EDAM:0000008 ! Undefined
 
 
+!
+! Topic<-Proteins<-Protein function
+!
+[Term]
+id: EDAM:0002276
+name: Protein function prediction
+namespace: topic
+def: "Predict general functional properties of a protein." [EDAM:EBI "EMBRACE definition"]
+xref: BioCatalogue:Function Prediction
+is_a: EDAM:0001775 ! Protein function
+relationship: concerns EDAM:0000008 ! Undefined
 
 !
-! Topic<-Protein analysis<-Protein domains
+! Topic<-Proteins<-Protein domains
 !
 
 
 
 
 !
-! Topic<-Protein analysis<-Protein interactions
+! Topic<-Proteins<-Protein interactions
 !
 [Term]
 id: EDAM:0000147
@@ -2106,6 +2143,7 @@ id: EDAM:0000148
 name: Protein-ligand interactions
 namespace: topic
 def: "Study protein-ligand (small molecule) interactions." [EDAM:EBI "EMBRACE definition"]
+xref: BioCatalogue:Ligand Interaction
 is_a: EDAM:0000128 ! Protein interactions
 relationship: concerns EDAM:0000008 ! Undefined
 
@@ -2122,12 +2160,12 @@ relationship: concerns EDAM:0000008 ! Undefined
 
 
 !
-! Topic<-Protein analysis<-Protein classification
+! Topic<-Proteins<-Protein classification
 !
 
 
 !
-! Topic<-Protein analysis<-Protein folding, stability and design
+! Topic<-Proteins<-Protein folding, stability and design
 !
 
 [Term]
@@ -2143,48 +2181,58 @@ relationship: concerns EDAM:0000008 ! Undefined
 
 
 !
-! Topic<-Protein analysis<-Transmembrane protein analysis
+! Topic<-Proteins<-Transmembrane proteins
 !
 [Term]
 id: EDAM:0000151
-name: G protein-coupled receptor (GPCR) analysis
+name: G protein-coupled receptors (GPCR)
 namespace: topic
 def: "Study G-protein coupled receptors (GPCRs)." [EDAM:EBI  "EMBRACE definition"]
-is_a: EDAM:0000131 ! Transmembrane protein analysis
+is_a: EDAM:0000131 ! Transmembrane proteins
+relationship: concerns EDAM:0000008 ! Undefined
+
+[Term]
+id: EDAM:0002278
+name: Transmembrane protein prediction
+namespace: topic
+def: "Predict transmembrane domains and topolgy in protein sequences." [EDAM:EBI  "EMBRACE definition"]
+is_a: EDAM:0000131 ! Transmembrane proteins
+is_a: EDAM:0000178 ! Protein secondary structure prediction
 relationship: concerns EDAM:0000008 ! Undefined
 
 
+
 !
-! Topic<-Protein analysis<-Enzymes
+! Topic<-Proteins<-Enzymes
 !
 
 
 
 !
-! Topic<-Metabolite analysis
+! Topic<-Metabolites
 !
 [Term]
 id: EDAM:0000152
-name: Carbohydrates analysis
+name: Carbohydrates
 namespace: topic
 def: "Carbohydrate data and analysis." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000079 ! Metabolite analysis
+is_a: EDAM:0000079 ! Metabolites
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
 id: EDAM:0000153
-name: Lipid analysis
+name: Lipids
 namespace: topic
 def: "Lipid data and analysis." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000079 ! Metabolite analysis
+is_a: EDAM:0000079 ! Metabolites
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
 id: EDAM:0000154
-name: Small molecules analysis
+name: Small molecules
 namespace: topic
-def: "Small molecules data and analysis." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000079 ! Metabolite analysis
+def: "Small molecule data and analysis." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0000079 ! Metabolites
 relationship: concerns EDAM:0000008 ! Undefined
 
 
@@ -2197,10 +2245,10 @@ relationship: concerns EDAM:0000008 ! Undefined
 !
 [Term]
 id: EDAM:0000155
-name: Sequence retrieval
+name: Sequence search and retrieval
 namespace: topic
 def: "Search or query a database and retrieve molecular sequences and associated data." [EDAM:EBI "EMBRACE definition"]
-comment: This refers to direct retrieval methods (e.g. the dbfetch program) which do not perform sequence similarity calculations.
+xref: BioCatalogue:Sequence Retrieval
 is_a: EDAM:0000080 ! Sequence analysis
 is_a: EDAM:0000090 ! Database search and retrieval
 relationship: concerns EDAM:0000008 ! Undefined
@@ -2232,6 +2280,17 @@ is_a: EDAM:0000080 ! Sequence analysis
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
+id: EDAM:0000188
+name: Sequence profiles and HMMs
+namespace: topic
+def: "Generate, manipulate, analyse or use some type of sequence profile (representing a sequence alignment)." [EDAM:EBI "EMBRACE definition"]
+comment: Profiles include position-specific scoring matrix (position weight matrix), hidden Markov models etc.
+is_a: EDAM:0000080 ! Sequence analysis
+is_a: EDAM:0000182 ! Sequence alignment
+relationship: concerns EDAM:0000008 ! Undefined
+
+
+[Term]
 id: EDAM:0000159
 name: Sequence comparison
 namespace: topic
@@ -2250,7 +2309,7 @@ relationship: concerns EDAM:0000008 ! Undefined
 
 
 !
-! Topic<-Sequence analysis<-Sequence retrieval
+! Topic<-Sequence analysis<-Sequence search and retrieval
 !
 
 
@@ -2263,6 +2322,24 @@ relationship: concerns EDAM:0000008 ! Undefined
 !
 ! Topic<-Sequence analysis<-Sequence composition
 !
+[Term]
+id: EDAM:0002262
+name: Repeat sequences
+namespace: topic
+def: "Analyse the repetitive nature of a molecular sequence." [EDAM:EBI "EMBRACE definition"]
+xref: BioCatalogue:Repeats
+is_a: EDAM:0000157 ! Sequence composition
+relationship: concerns EDAM:0000008 ! Undefined
+
+[Term]
+id: EDAM:0002263
+name: Sequence complexity
+namespace: topic
+def: "Analyse the complexity of a molecular sequence." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0000157 ! Sequence composition
+relationship: concerns EDAM:0000008 ! Undefined
+
+
 
 !
 ! Topic<-Sequence analysis<-Sequence motifs
@@ -2272,6 +2349,7 @@ id: EDAM:0000161
 name: Protein sequence motifs
 namespace: topic
 def: "Discover, identify or analyse motifs or conserved patterns in protein sequences." [EDAM:EBI "EMBRACE definition"]
+xref: BioCatalogue:Motifs
 is_a: EDAM:0000158 ! Sequence motifs
 relationship: concerns EDAM:0000008 ! Undefined
 
@@ -2285,14 +2363,21 @@ relationship: concerns EDAM:0000008 ! Undefined
 
 
 !
+! Topic<-Sequence analysis<Sequence profiles and HMMs
+!
+
+
+!
 ! Topic<-Sequence analysis<-Sequence comparison
 !
 [Term]
 id: EDAM:0000163
 name: Sequence similarity search
 namespace: topic
-def: "Search for and retrieve molecular sequences that are similar to a query." [EDAM:EBI "EMBRACE definition"]
+def: "Search for and retrieve molecular sequences that are similar to a sequence-based query (typically a simple sequence)." [EDAM:EBI "EMBRACE definition"]
+comment: The query is a sequence-based entity such as another sequence, a motif or profile.
 is_a: EDAM:0000159 ! Sequence comparison
+is_a: EDAM:0000155 ! Sequence search and retrieval
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
@@ -2303,6 +2388,28 @@ def: "Compare and cluster multiple sequences on the basis of similarity, process
 is_a: EDAM:0000159 ! Sequence comparison
 relationship: concerns EDAM:0000008 ! Undefined
 
+[Term]
+id: EDAM:0002260
+name: Protein sequence comparison
+namespace: topic
+def: "Compare two or more protein sequences." [EDAM:EBI "EMBRACE definition"]
+comment: Use this term for methods that are exclusively for protein sequences.
+xref: BioCatalogue:Protein Sequence Similarity
+is_a: EDAM:0000159 ! Sequence comparison
+is_a: EDAM:0000125 ! Protein sequence analysis
+relationship: concerns EDAM:0000008 ! Undefined
+
+[Term]
+id: EDAM:0002261
+name: Nucleic acid sequence comparison
+namespace: topic
+def: "Compare two or more nucleotide sequences." [EDAM:EBI "EMBRACE definition"]
+comment: Use this term for methods that are exclusively for nucleotide sequences.
+xref: BioCatalogue:Nucleotide Sequence Similarity
+is_a: EDAM:0000159 ! Sequence comparison
+is_a: EDAM:0000096 ! Nucleic acid sequence analysis
+relationship: concerns EDAM:0000008 ! Undefined
+
 !
 ! Topic<-Sequence analysis<-Sequence features
 !
@@ -2316,22 +2423,23 @@ relationship: concerns EDAM:0000008 ! Undefined
 !
 [Term]
 id: EDAM:0000165
-name: Structure retrieval
+name: Structure search and retrieval
 namespace: topic
 def: "Search or query a database and retrieve molecular structures." [EDAM:EBI "EMBRACE definition"]
-comment: This refers to direct retrieval methods which do not perform calculations on the structure.
+xref: BioCatalogue:Structure Retrieval
 is_a: EDAM:0000081 ! Structure analysis
 is_a: EDAM:0000090 ! Database search and retrieval
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
 id: EDAM:0000166
-name: Structural motifs
+name: Protein structural motifs
 namespace: topic
-def: "Discover, identify or analyse common 3D motifs in molecular structures." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000081 ! Structure analysis
+def: "Discover, identify, predict or analyse structural features or common 3D motifs of protein structures." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0002125 ! Protein tertiary structure analysis
 relationship: concerns EDAM:0000008 ! Undefined
 
+
 [Term]
 id: EDAM:0000167
 name: Structural profiles
@@ -2350,19 +2458,16 @@ relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
 id: EDAM:0000170
-name: Structural features
+name: Structural features and motifs
 namespace: topic
-def: "Handle, predict or analyse structural features of molecules(s)." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000081 ! Structure analysis
-relationship: concerns EDAM:0000008 ! Undefined
+def: "Discover, identify, predict or analyse structural features and common motifs of molecular structures." [EDAM:EBI "EMBRACE definition"]
+is_obsolete: true
+consider: EDAM:0000166 ! Protein structural motifs
 
 !
-! Topic<-Structure analysis<-Structure retrieval
+! Topic<-Structure analysis<-Structure search and retrieval
 !
 
-!
-! Topic<-Structure analysis<-Structural motifs
-!
 
 
 !
@@ -2377,8 +2482,9 @@ relationship: concerns EDAM:0000008 ! Undefined
 id: EDAM:0000168
 name: Secondary structure comparison
 namespace: topic
-def: "Compare two or more molecular secondary structures." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0001770 ! Structure comparison
+def: "Compare two or more protein secondary structures." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0000143 ! Protein structure comparison
+is_a: EDAM:0002124 ! Protein secondary structure analysis
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
@@ -2386,9 +2492,19 @@ id: EDAM:0000169
 name: Tertiary structure comparison
 namespace: topic
 def: "Compare two or more molecular tertiary (3D) structures." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0001770 ! Structure comparison
+is_a: EDAM:0000143 ! Protein structure comparison
+is_a: EDAM:0002125 ! Protein tertiary structure analysis
 relationship: concerns EDAM:0000008 ! Undefined
 
+[Term]
+id: EDAM:0002271
+name: Structure similarity search
+namespace: topic
+def: "Search for and retrieve molecular structures that are similar to a structure-based query (typically another structure or part of a structure)." [EDAM:EBI "EMBRACE definition"]
+comment: The query is a structure-based entity such as another structure, a 3D (structural) motif, 3D profile or template.
+is_a: EDAM:0001770 ! Structure comparison
+is_a: EDAM:0000165 ! Structure search and retrieval
+relationship: concerns EDAM:0000008 ! Undefined
 
 
 !
@@ -2400,7 +2516,7 @@ relationship: concerns EDAM:0000008 ! Undefined
 !
 
 !
-! Topic<-Structure analysis<-Structural features
+! Topic<-Structure analysis<-Structural features and motifs
 !
 
 
@@ -2413,91 +2529,94 @@ id: EDAM:0000171
 name: Tertiary structure prediction
 namespace: topic
 def: "Predict protein or nucleic acid tertiary (3D) structure." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000082 ! Structure prediction
-relationship: concerns EDAM:0000008 ! Undefined
+is_obsolete: true
+consider: EDAM:0000082 ! Structure prediction
 
 [Term]
 id: EDAM:0000172
 name: Protein structure prediction
 namespace: topic
 def: "Predict secondary or tertiary structure or other structural features of protein sequences." [EDAM:EBI "EMBRACE definition"]
+xref: BioCatalogue:Protein Structure Prediction
 is_a: EDAM:0000082 ! Structure prediction
-is_a: EDAM:0000078 ! Protein analysis
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
 id: EDAM:0000173
 name: Nucleic acid structure prediction
 namespace: topic
-def: "Predict secondary or tertiary structure of nucleic acids." [EDAM:EBI "EMBRACE definition"]
+def: "Predict or design secondary or tertiary structure of nucleic acids (typically RNA)." [EDAM:EBI "EMBRACE definition"]
+xref: BioCatalogue:Nucleotide Structure Prediction
+xref: BioCatalogue:Nucleotide Secondary Structure
+xref: BioCatalogue:Nucleotide Tertiary Structure
 is_a: EDAM:0000082 ! Structure prediction
-is_a: EDAM:0000077 ! Nucleic acid analysis
+is_a: EDAM:0000097 ! Nucleic acid structure analysis
 relationship: concerns EDAM:0000008 ! Undefined
 
 
-
-
-
-!
-! Topic<-Structure prediction<-Tertiary structure prediction
-!
-
 [Term]
 id: EDAM:0000174
 name: Ab initio structure prediction
 namespace: topic
-def: "Predict three-dimensional structure of a molecular sequence from first principles, using a physics-based or empirical scoring function and without using explicit structural templates." [EDAM:EBI "EMBRACE definition"]
+def: "Predict three-dimensional structure of a protein sequence from first principles, using a physics-based or empirical scoring function and without using explicit structural templates." [EDAM:EBI "EMBRACE definition"]
 synonym: "de novo protein structure prediction" EXACT []
-is_a: EDAM:0000171 ! Tertiary structure prediction
-is_a: EDAM:0002125 ! Protein tertiary structure analysis
+is_a: EDAM:0000179 ! Protein tertiary structure prediction
+relationship: concerns EDAM:0000008 ! Undefined
+
+[Term]
+id: EDAM:0002275
+name: Molecular modelling
+namespace: topic
+def: "Build or assess a model of a molecules properties or behaviour using computational methods. " [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0000082 ! Structure prediction
+is_a: EDAM:0000082 ! 
 relationship: concerns EDAM:0000008 ! Undefined
 
 
 [Term]
 id: EDAM:0000175
-name: Molecular modelling
+name: Homology modelling
 namespace: topic
-def: "Build or assess a three-dimensional molecular model using known sequence and structural data." [EDAM:EBI "EMBRACE definition"]
+def: "Build or assess a three-dimensional protein model using known sequence and structural data." [EDAM:EBI "EMBRACE definition"]
 comment: Molecular modelling methods might use sequence-structure alignment, structural templates, molecular dynamics, energy minimization etc.
 synonym: "Comparative modelling" EXACT []
-is_a: EDAM:0000171 ! Tertiary structure prediction
-is_a: EDAM:0002125 ! Protein tertiary structure analysis
+is_a: EDAM:0000179 ! Protein tertiary structure prediction
+is_a: EDAM:0002275 ! Molecular modelling
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
 id: EDAM:0000176
 name: Molecular dynamics
 namespace: topic
-def: "Simulate protein conformation using molecular dynamics." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000171 ! Tertiary structure prediction
-is_a: EDAM:0002125 ! Protein tertiary structure analysis
+def: "Simulate molecular (typically protein) conformation using a computational model of physicalal forces and computer simulation." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0002275 ! Molecular modelling
+is_a: EDAM:0000179 ! Protein tertiary structure prediction
 relationship: concerns EDAM:0000008 ! Undefined
 
 
 !
-! Topic<-Structure prediction<-Tertiary structure prediction<-Ab initio structure prediction
+! Topic<-Structure prediction<-Ab initio structure prediction
 !
 
 !
-! Topic<-Structure prediction<-Tertiary structure prediction<-Molecular modelling
+! Topic<-Structure prediction<-Molecular modelling
 !
 [Term]
 id: EDAM:0000177
 name: Protein docking
 namespace: topic
 def: "Model the structure of a protein in complex with a small molecule or another macromolecule." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000175 ! Molecular modelling
-is_a: EDAM:0000179 ! Protein tertiary structure prediction
+is_a: EDAM:0002275 ! Molecular modelling
 relationship: concerns EDAM:0000008 ! Undefined
 
 
 
 !
-! Topic<-Structure prediction<-Tertiary structure prediction<-Molecular dynamics
+! Topic<-Structure prediction<-Molecular dynamics
 !
 
 !
-! Topic<-Structure prediction<-Tertiary structure prediction<-Protein docking
+! Topic<-Structure prediction<-Protein docking
 !
 
 
@@ -2510,6 +2629,7 @@ id: EDAM:0000178
 name: Protein secondary structure prediction
 namespace: topic
 def: "Predict secondary or supersecondary structure of protein sequences." [EDAM:EBI "EMBRACE definition"]
+xref: BioCatalogue:Protein Secondary Structure
 is_a: EDAM:0000172 ! Protein structure prediction
 is_a: EDAM:0002124 ! Protein secondary structure analysis
 relationship: concerns EDAM:0000008 ! Undefined
@@ -2519,8 +2639,8 @@ id: EDAM:0000179
 name: Protein tertiary structure prediction
 namespace: topic
 def: "Predict tertiary structure of protein sequences." [EDAM:EBI "EMBRACE definition"]
+xref: BioCatalogue:Protein Tertiary Structure
 is_a: EDAM:0000172 ! Protein structure prediction
-is_a: EDAM:0000171 ! Tertiary structure prediction
 is_a: EDAM:0002125 ! Protein tertiary structure analysis
 relationship: concerns EDAM:0000008 ! Undefined
 
@@ -2529,9 +2649,7 @@ id: EDAM:0000180
 name: Protein fold recognition
 namespace: topic
 def: "Recognize (predict and assign) known protein structural domains or folds in protein sequence(s)." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000172 ! Protein structure prediction
-is_a: EDAM:0000129 ! Protein classification
-is_a: EDAM:0002125 ! Protein tertiary structure analysis
+is_a: EDAM:0000179 ! Protein tertiary structure prediction
 relationship: concerns EDAM:0000008 ! Undefined
 
 !
@@ -2542,13 +2660,14 @@ id: EDAM:0000181
 name: RNA structure prediction
 namespace: topic
 def: "Predict or design secondary or tertiary structure of RNA." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000173 ! Nucleic acid structure prediction
-is_a: EDAM:0000099 ! RNA analysis
-relationship: concerns EDAM:0000008 ! Undefined
+is_obsolete: true
+consider: EDAM:0000173 ! Nucleic acid structure prediction
+is_a: EDAM:0000099 ! RNA
+
 
 
 !
-! Topic<-Structure prediction<-Molecular modelling
+! Topic<-Structure prediction<-Homology modelling
 !
 
 
@@ -2563,16 +2682,28 @@ relationship: concerns EDAM:0000008 ! Undefined
 id: EDAM:0000182
 name: Sequence alignment
 namespace: topic
-def: "Alignment of molecular sequences or sequence profiles (representing sequence alignments)." [EDAM:EBI "EMBRACE definition"]
+def: "Generate or analyse alignments of molecular sequences or sequence profiles (representing sequence alignments)." [EDAM:EBI "EMBRACE definition"]
+xref: BioCatalogue:Protein Sequence Alignment
+xref: BioCatalogue:Nucleotide Sequence Alignment
+is_a: EDAM:0000083 ! Alignment
+is_a: EDAM:0000159 ! Sequence comparison
+relationship: concerns EDAM:0000008 ! Undefined
+
+[Term]
+id: EDAM:0002283
+name: Sequence profile alignment
+namespace: topic
+def: "Generate or analyse alignments involving ." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000083 ! Alignment
 is_a: EDAM:0000159 ! Sequence comparison
+is_a: EDAM:0000188 ! Sequence profiles and HMMs
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
 id: EDAM:0000183
 name: Structure alignment
 namespace: topic
-def: "Alignment (superimposition) of molecular tertiary structures or structural (3D) profiles (representing a structure or structure alignment)." [EDAM:EBI "EMBRACE definition"]
+def: "Generate or analyse alignments (superimpositions) of molecular tertiary structures or structural (3D) profiles (representing a structure or structure alignment)." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000083 ! Alignment
 is_a: EDAM:0000169 ! Tertiary structure comparison
 relationship: concerns EDAM:0000008 ! Undefined
@@ -2581,9 +2712,10 @@ relationship: concerns EDAM:0000008 ! Undefined
 id: EDAM:0000184
 name: Sequence-structure alignment
 namespace: topic
-def: "Alignment of molecular sequence to structure or to structural (3D) profiles or templates (representing a structure or structure alignment)." [EDAM:EBI "EMBRACE definition"]
+def: "Generate or analyse alignments of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment)." [EDAM:EBI "EMBRACE definition"]
+synonym: "Threading" EXACT []
 is_a: EDAM:0000083 ! Alignment
-is_a: EDAM:0000159 ! Sequence comparison
+is_a: EDAM:0000175 ! Homology modelling
 relationship: concerns EDAM:0000008 ! Undefined
 
 
@@ -2597,7 +2729,9 @@ relationship: concerns EDAM:0000008 ! Undefined
 id: EDAM:0000185
 name: Pairwise sequence alignment
 namespace: topic
-def: "Alignment of exactly two molecular sequences or sequence profiles (representing sequence alignments)." [EDAM:EBI "EMBRACE definition"]
+def: "Align exactly two molecular sequences or sequence profiles (representing sequence alignments)." [EDAM:EBI "EMBRACE definition"]
+xref: BioCatalogue:Protein Pairwise Alignment
+xref: BioCatalogue:Nucleotide Pairwise Alignment
 is_a: EDAM:0000182 ! Sequence alignment
 relationship: concerns EDAM:0000008 ! Undefined
 
@@ -2605,7 +2739,9 @@ relationship: concerns EDAM:0000008 ! Undefined
 id: EDAM:0000186
 name: Multiple sequence alignment
 namespace: topic
-def: "Alignment of two or more molecular sequences or sequence profiles (representing sequence alignments)." [EDAM:EBI "EMBRACE definition"]
+def: "Align two or more molecular sequences or sequence profiles (representing sequence alignments)." [EDAM:EBI "EMBRACE definition"]
+xref: BioCatalogue:Protein Multiple Alignment
+xref: BioCatalogue:Nucleotide Multiple Alignment
 is_a: EDAM:0000182 ! Sequence alignment
 relationship: concerns EDAM:0000008 ! Undefined
 
@@ -2618,19 +2754,10 @@ is_a: EDAM:0000182 ! Sequence alignment
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
-id: EDAM:0000188
-name: Sequence profiles
-namespace: topic
-def: "Generate, manipulate, analyse or use some type of sequence profile (representing a sequence alignment)." [EDAM:EBI "EMBRACE definition"]
-comment: Profiles include position-specific scoring matrix (position weight matrix), hidden Markov models etc.
-is_a: EDAM:0000182 ! Sequence alignment
-relationship: concerns EDAM:0000008 ! Undefined
-
-[Term]
 id: EDAM:0000189
 name: Structure-based sequence alignment
 namespace: topic
-def: "Alignment of molecular sequences using sequence and structural information." [EDAM:EBI "EMBRACE definition"]
+def: "Align molecular sequences using sequence and structural information." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000182 ! Sequence alignment
 relationship: concerns EDAM:0000008 ! Undefined
 
@@ -2644,9 +2771,28 @@ name: Structure alignment analysis
 namespace: topic
 def: "Analyse or compare alignments of molecular structures or structural (3D) profiles (representing a structure or structure alignment)." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000183 ! Structure alignment
-is_a: EDAM:0000169 ! Tertiary structure comparison
 relationship: concerns EDAM:0000008 ! Undefined
 
+[Term]
+id: EDAM:0002272
+name: Multiple structure alignment
+namespace: topic
+def: "Align (superimpose) two or more molecular tertiary structures or structural (3D) profiles (representing a structure or structure alignment)." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0000183 ! Structure alignment
+relationship: concerns EDAM:0000008 ! Undefined
+
+[Term]
+id: EDAM:0002273
+name: Pairwise structure alignment
+namespace: topic
+def: "Align (superimpose) exactly two molecular tertiary structures or structural (3D) profiles (representing a structure or structure alignment)." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0000183 ! Structure alignment
+relationship: concerns EDAM:0000008 ! Undefined
+
+
+
+
+
 
 !
 ! Topic<-Alignment<Sequence-structure alignment
@@ -2660,9 +2806,6 @@ relationship: concerns EDAM:0000008 ! Undefined
 ! Topic<-Alignment<Structure alignment analysis
 !
 
-!
-! Topic<-Alignment<Sequence profiles
-!
 
 
 !
@@ -2673,12 +2816,23 @@ id: EDAM:0000191
 name: Phylogeny reconstruction
 namespace: topic
 def: "Reconstruct a phylogeny, for example, by building a phylogenetic tree." [EDAM:EBI "EMBRACE definition"]
+xref: BioCatalogue:Tree Inference
+xref: BioCatalogue:Evolutionary Distance Measurements
+is_a: EDAM:0000084 ! Phylogenetics
+relationship: concerns EDAM:0000008 ! Undefined
+
+[Term]
+id: EDAM:0002257
+name: Phylogeny visualisation
+namespace: topic
+def: "Visualise a phylogeny, for example, render a phylogenetic tree." [EDAM:EBI "EMBRACE definition"]
+xref: BioCatalogue:Tree Display
 is_a: EDAM:0000084 ! Phylogenetics
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
 id: EDAM:0000192
-name: Phylogenetic tree simulation
+name: Phylogenetic simulation
 namespace: topic
 def: "Simulate DNA sequence evolution, a phylogenetic tree or the underlying data." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000084 ! Phylogenetics
@@ -2698,6 +2852,7 @@ name: Phylogenomics
 namespace: topic
 def: "Analyse phylogenetic and genomic data simultaneously." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000084 ! Phylogenetics
+is_a: EDAM:0000093 ! Genomics
 relationship: concerns EDAM:0000008 ! Undefined
 
 
@@ -2716,15 +2871,15 @@ relationship: concerns EDAM:0000008 ! Undefined
 !
 
 !
-! Topic<-Genomics<-Sequencing
+! Topic<-Genomics<-Sequencing and mapping
 !
 [Term]
 id: EDAM:0000195
 name: Polymerase chain reaction
 namespace: topic
-def: "Data and analysis concerning polymerase chain reaction (PCR), for example, design assays or primers or perform virtual PCR." [EDAM:EBI "EMBRACE definition"]
+def: "Handle or analyse data concerning polymerase chain reaction (PCR), for example, design assays or primers or perform virtual PCR." [EDAM:EBI "EMBRACE definition"]
 synonym: "PCR" EXACT []
-is_a: EDAM:0000102 ! Sequencing
+is_a: EDAM:0000102 ! Sequencing and mapping
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
@@ -2732,7 +2887,7 @@ id: EDAM:0000196
 name: Sequence assembly
 namespace: topic
 def: "Assemble fragments of a DNA sequence to reconstruct the original sequence." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000102 ! Sequencing
+is_a: EDAM:0000102 ! Sequencing and mapping
 relationship: concerns EDAM:0000008 ! Undefined
 
 
@@ -2744,6 +2899,66 @@ relationship: concerns EDAM:0000008 ! Undefined
 
 
 
+!
+! Topic<-Proteomics
+!
+[Term]
+id: EDAM:0000133
+name: Two-dimensional gel electrophoresis
+namespace: topic
+def: "Handle two-dimensional gel electrophoresis data." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0000121 ! Proteomics
+relationship: concerns EDAM:0000008 ! Undefined
+
+
+[Term]
+id: EDAM:0000134
+name: Mass spectrometry
+namespace: topic
+def: "Handle mass spectrometry and related data." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0000121 ! Proteomics
+relationship: concerns EDAM:0000008 ! Undefined
+
+[Term]
+id: EDAM:0000135
+name: Protein microarrays
+namespace: topic
+def: "Protein microarray data and analysis." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0000121 ! Proteomics
+is_a: EDAM:0000200 ! Microarrays
+relationship: concerns EDAM:0000008 ! Undefined
+
+!
+! Topic<-Genomics
+!
+[Term]
+id: EDAM:0000101
+name: Comparative genomics
+namespace: topic
+def: "Compare the structure or function of multiple genomes." [EDAM:EBI "EMBRACE definition"]
+xref: BioCatalogue:Comparative Genomics
+is_a: EDAM:0000093 ! Genomics
+relationship: concerns EDAM:0000008 ! Undefined
+
+[Term]
+id: EDAM:0000102
+name: Sequencing and mapping
+namespace: topic
+def: "Determine and map complete nucleotide sequences." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0000093 ! Genomics
+is_a: EDAM:0000003 ! Topic
+relationship: concerns EDAM:0000008 ! Undefined
+
+[Term]
+id: EDAM:0000103
+name: Genetic mapping
+namespace: topic
+def: "Identify, map or analyse genetic markers in DNA sequences, for example the genetic (linkage) map for a chromosome." [EDAM:EBI "EMBRACE definition"]
+synonym: "Genetic linkage" EXACT []
+synonym: "Linkage mapping" EXACT []
+is_a: EDAM:0000102 ! Sequencing and mapping
+relationship: concerns EDAM:0000008 ! Undefined
+
 
 
 
@@ -2754,7 +2969,8 @@ relationship: concerns EDAM:0000008 ! Undefined
 id: EDAM:0000197
 name: Gene expression
 namespace: topic
-def: "Data and analysis concerning gene expression." [EDAM:EBI "EMBRACE definition"]
+def: "Handle or analyse gene expression data." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0000003 ! Topic
 is_a: EDAM:0000085 ! Functional genomics
 relationship: concerns EDAM:0000008 ! Undefined
 
@@ -2762,7 +2978,10 @@ relationship: concerns EDAM:0000008 ! Undefined
 id: EDAM:0000198
 name: Biological pathways
 namespace: topic
-def: "Identify, predict, model or analyse metabolic or other biochemical pathways, or metabolites such as sugars and lipids." [EDAM:EBI "EMBRACE definition"]
+def: "Identify, predict, model or analyse metabolic or other biological pathways." [EDAM:EBI "EMBRACE definition"]
+xref: BioCatalogue:Pathways
+xref: BioCatalogue:Pathway Retrieval
+is_a: EDAM:0000003 ! Topic
 is_a: EDAM:0000085 ! Functional genomics
 relationship: concerns EDAM:0000008 ! Undefined
 
@@ -2770,33 +2989,25 @@ relationship: concerns EDAM:0000008 ! Undefined
 id: EDAM:0000199
 name: Mutation and polymorphism
 namespace: topic
-def: "Data and analysis on mutation and polymorphism, for example single nucleotide polymorphisms (SNPs)." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000085 ! Functional genomics
+def: "Handle or analyse mutation and polymorphism data." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0000003 ! Topic
 is_a: EDAM:0000096 ! Nucleic acid sequence analysis
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
-id: EDAM:0000200
-name: Microarrays
-namespace: topic
-def: "Process, analyse, interpret and visualise microarray data or design probes and experiments." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000085 ! Functional genomics
-relationship: concerns EDAM:0000008 ! Undefined
-
-[Term]
 id: EDAM:0000201
-name: Immunological analysis
+name: Immunology
 namespace: topic
 def: "Immunological data and analysis." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000085 ! Functional genomics
+is_a: EDAM:0000003 ! Topic
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
 id: EDAM:0000202
-name: Pharmacological analysis
+name: Pharmacology
 namespace: topic
 def: "Data and analysis concerning drugs." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000085 ! Functional genomics
+is_a: EDAM:0000003 ! Topic
 relationship: concerns EDAM:0000008 ! Undefined
 
 
@@ -2809,10 +3020,9 @@ relationship: concerns EDAM:0000008 ! Undefined
 id: EDAM:0000203
 name: Expression profiling
 namespace: topic
-def: "Analyse the expression level of mRNA by identifying, quantifying, comparing or analysing mRNA transcripts." [EDAM:EBI "EMBRACE definition"]
+def: "Analyse the expression level of mRNA by identifying, quantifying or comparing mRNA transcripts." [EDAM:EBI "EMBRACE definition"]
 synonym: "Transcriptomics" EXACT []
 is_a: EDAM:0000197 ! Gene expression
-is_a: EDAM:0000099 ! RNA analysis
 relationship: concerns EDAM:0000008 ! Undefined
 
 
@@ -2820,34 +3030,65 @@ relationship: concerns EDAM:0000008 ! Undefined
 id: EDAM:0000204
 name: Gene regulation
 namespace: topic
-def: "The study of the regulation of gene expression." [EDAM:EBI "EMBRACE definition"]
+def: "Study the regulation of gene expression." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000197 ! Gene expression
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
 id: EDAM:0000205
-name: EST and cDNA sequence analysis
+name: EST and cDNA
 namespace: topic
-def: "Analyse or process expressed sequence tag (EST) sequences, complementary DNA (cDNA) sequences." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000197 ! Gene expression
-is_a: EDAM:0000096 ! Nucleic acid sequence analysis
-relationship: concerns EDAM:0000008 ! Undefined
+def: "Handle or analyse expressed sequence tag (EST) or complementary DNA (cDNA) sequences." [EDAM:EBI "EMBRACE definition"]
+is_obsolete: true
+consider: EDAM:0000197 ! Gene expression
 
 
 
 
 ! Topic<-Functional genomics<-Biological pathways
 !
+[Term]
+id: EDAM:0002274
+name: Pathway search and retrieval
+namespace: topic
+def: "Search or query a database and retrieve a biological pathway or associated data." [EDAM:EBI "EMBRACE definition"]
+xref: BioCatalogue:Pathway Retrieval
+is_a: EDAM:0000090 ! Database search and retrieval
+is_a: EDAM:0000198 ! Biological pathways
+relationship: concerns EDAM:0000008 ! Undefined
 
 
 !
 ! Topic<-Functional genomics<-Mutation and polymorphism
 !
+[Term]
+id: EDAM:0002277
+name: SNPs
+namespace: topic
+def: "Identify, analyse and handle single nucleotide polymorphisms (SNP) and associated data." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0000199 ! Mutation and polymorphism
+relationship: concerns EDAM:0000008 ! Undefined
+
+
+
+!
+! Topic<-Structural genomics
+!
+[Term]
+id: EDAM:0000136
+name: Raw structural data analysis
+namespace: topic
+def: "Assign, validate or refine a molecular (tpyically protein) structure from raw data from X-ray crystallography or nuclear magnetic resonance (NMR) and circular dichroism (CD) spectroscopy." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0000122 ! Structural genomics
+is_a: EDAM:0000126 ! Protein structure analysis
+is_a: EDAM:0002275 ! Molecular modelling
+relationship: concerns EDAM:0000008 ! Undefined
+
 
 
 
 !
-! Topic<-Functional genomics<-Microarrays
+! Topic<-Microarrays
 !
 [Term]
 id: EDAM:0000206
@@ -2855,11 +3096,10 @@ name: DNA microarrays
 namespace: topic
 def: "DNA microarray data and analysis." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000200 ! Microarrays
-is_a: EDAM:0000197 ! Gene expression
 relationship: concerns EDAM:0000008 ! Undefined
 
 !
-! Topic<-Functional genomics<-Microarrays<-DNA microarrays
+! Topic<-Microarrays<-DNA microarrays
 !
 [Term]
 id: EDAM:0000207
@@ -2867,25 +3107,24 @@ name: DNA microarray probes
 namespace: topic
 def: "Design or analyse DNA microarray probes." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000200 ! Microarrays
-is_a: EDAM:0000197 ! Gene expression
 relationship: concerns EDAM:0000008 ! Undefined
 
 
 
 
 !
-! Topic<-Functional genomics<-Immunological analysis
+! Topic<-Functional genomics<-Immunology
 !
 
 !
-! Topic<-Functional genomics<-Pharmacological analysis
+! Topic<-Functional genomics<-Pharmacology
 !
 [Term]
 id: EDAM:0000208
 name: Pharmacogenomics
 namespace: topic
 def: "Analyse the influence of genotype on drug response, for example by correlating gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000202 ! Pharmacological analysis
+is_a: EDAM:0000202 ! Pharmacology
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
@@ -2894,7 +3133,7 @@ name: Drug design
 namespace: topic
 def: "Search for, analyse or design drugs or potential drug compounds." [EDAM:EBI "EMBRACE definition"]
 comment: This includes methods that search compound collections, identify or search a database of antimicrobial peptides, generate or analyse druG 3D conformations, identify drug targets with structural docking etc.
-is_a: EDAM:0000202 ! Pharmacological analysis
+is_a: EDAM:0000202 ! Pharmacology
 relationship: concerns EDAM:0000008 ! Undefined
 
 
@@ -2983,15 +3222,22 @@ id: EDAM:0000217
 name: Literature search
 namespace: topic
 def: "Query the biomedical and informatics literature." [EDAM:EBI "EMBRACE definition"]
+xref: BioCatalogue: Document Discovery
+xref: BioCatalogue: Literature retrieval
 is_a: EDAM:0000088 ! Literature and documentation
+is_a: EDAM:0000090 ! Database search and retrieval
 relationship: concerns EDAM:0000008 ! Undefined
 
 [Term]
 id: EDAM:0000218
 name: Text mining
 namespace: topic
-def: "Process and analyse the biomedical and informatics literature to extract information from it." [EDAM:EBI "EMBRACE definition"]
+def: "Analyse the biomedical and informatics literature and extract information." [EDAM:EBI "EMBRACE definition"]
 synonym: "Text data mining" EXACT []
+xref: BioCatalogue:Text Mining
+xref: BioCatalogue:Document Similarity
+xref: BioCatalogue:Document Clustering
+xref: BioCatalogue:Named Entity Recognition
 is_a: EDAM:0000088 ! Literature and documentation
 relationship: concerns EDAM:0000008 ! Undefined
 
@@ -3000,6 +3246,17 @@ relationship: concerns EDAM:0000008 ! Undefined
 !
 ! Topic<-Ontologies
 !
+[Term]
+id: EDAM:0002255
+name: Ontology lookup
+namespace: topic
+def: "Query a biomedical ontology, for example to look-up terms." [EDAM:EBI "EMBRACE definition"]
+xref: BioCatalogue:Ontology Lookup
+is_a: EDAM:0000089 ! Ontologies
+is_a: EDAM:0000090 ! Database search and retrieval
+relationship: concerns EDAM:0000008 ! Undefined
+
+
 
 
 !
@@ -3009,21 +3266,46 @@ relationship: concerns EDAM:0000008 ! Undefined
 
 
 !
-! Topic<-Database and file management
+! Topic<-Annotation
 !
 [Term]
-id: EDAM:0000219
-name: Annotation
+id: EDAM:0000221
+name: Sequence annotation
 namespace: topic
-def: "Annotate biological database entities." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000091 ! Database and file management
+def: "Annotate a molecular sequence." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0000219 ! Annotation
+is_a: EDAM:0000080 ! Sequence analysis
+relationship: concerns EDAM:0000008 ! Undefined
+
+[Term]
+id: EDAM:0000222
+name: Genome annotation
+namespace: topic
+def: "Annotate a genome." [EDAM:EBI "EMBRACE definition"]
+xref: BioCatalogue:Genome Annotation
+is_a: EDAM:0000219 ! Annotation
+is_a: EDAM:0000093 ! Genomics
+relationship: concerns EDAM:0000008 ! Undefined
+
+[Term]
+id: EDAM:0002256
+name: Ontology annotation
+namespace: topic
+def: "Annotate a biomedical ontology, for example add new terms." [EDAM:EBI "EMBRACE definition"]
+xref: BioCatalogue:Ontology Annotation
+is_a: EDAM:0000219 ! Annotation
+is_a: EDAM:0000089 ! Ontologies
 relationship: concerns EDAM:0000008 ! Undefined
 
+
+!
+! Topic<-Database and file management
+!
 [Term]
 id: EDAM:0000220
 name: File handling
 namespace: topic
-def: "Generate or handle a file of biological data, for example file format conversion, file debugging etc." [EDAM:EBI "EMBRACE definition"]
+def: "Generate or handle a file of biological data, for example file format conversion, file editing, debugging etc." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000091 ! Database and file management
 relationship: concerns EDAM:0000008 ! Undefined
 
@@ -3035,29 +3317,29 @@ def: "Submit an object to a database." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000091 ! Database and file management
 relationship: concerns EDAM:0000008 ! Undefined
 
+[Term]
+id: EDAM:0002270
+name: Database indexing
+namespace: topic
+def: "Create or analyse a database index." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0000091 ! Database and file management
+relationship: concerns EDAM:0000008 ! Undefined
 
 
 
 !
-! Topic<-Database and file management<-Annotation
+! Topic<-Database and file management<-File handling
 !
 [Term]
-id: EDAM:0000221
-name: Sequence annotation
+id: EDAM:0002286
+name: File format handling
 namespace: topic
-def: "Annotate a molecular sequence." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000219 ! Annotation
-is_a: EDAM:0000080 ! Sequence analysis
+def: "Handle file formatting tasks, for example file format conversion, transformation or validation." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0000220 ! File handling
 relationship: concerns EDAM:0000008 ! Undefined
 
-[Term]
-id: EDAM:0000222
-name: Genome annotation
-namespace: topic
-def: "Annotate a genome." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000219 ! Annotation
-is_a: EDAM:0000096 ! Nucleic acid sequence analysis
-relationship: concerns EDAM:0000008 ! Undefined
+
+
 
 
 
@@ -3075,8 +3357,32 @@ relationship: concerns EDAM:0000008 ! Undefined
 !
 
 
+!
+! Topic<-Chemoinformatics
+!
+
+!
+! Topic<-Systems biology and modelling
+!
 
+[Term]
+id: EDAM:0002267
+name: Biological model construction
+namespace: topic
+def: "Construct a biological model." [EDAM:EBI "EMBRACE definition"]
+xref: BioCatalogue:Model Creation
+is_a: EDAM:0002259 ! Systems biology and modelling 
+relationship: concerns EDAM:0000008 ! Undefined
 
+[Term]
+id: EDAM:0002268
+name: Biological model analysis
+namespace: topic
+def: "Analyse a biological model." [EDAM:EBI "EMBRACE definition"]
+xref: BioCatalogue:Model Analysis
+xref: BioCatalogue:Model Execution
+is_a: EDAM:0002259 ! Systems biology and modelling 
+relationship: concerns EDAM:0000008 ! Undefined
 
 
 
@@ -3134,7 +3440,6 @@ id: EDAM:0000225
 name: Database cross-reference retrieval
 namespace: operation
 def: "Search database to retrieve all relevant cross-references for a particular entity or entry." [EDAM:EBI "EMBRACE definition"]
-comment: For example
 is_a: EDAM:0000004 ! Operation
 relationship: is_concern_of EDAM:0000090 ! Database search and retrieval
 relationship: has_input EDAM:0000841 ! Undefined
@@ -3171,7 +3476,7 @@ name: Database indexing
 namespace: operation
 def: "Generate an index of a file of biological data." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000004 ! Operation
-relationship: is_concern_of EDAM:0000091 ! Database and file management
+relationship: is_concern_of EDAM:0002270 ! Database indexing
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000955 ! Database index
 
@@ -3181,7 +3486,7 @@ name: Database index analysis
 namespace: operation
 def: "Analyse an index of a file of biological data." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000004 ! Operation
-relationship: is_concern_of EDAM:0000091 ! Database and file management
+relationship: is_concern_of EDAM:0002270 ! Database indexing
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000956 ! Database index annotation
 
@@ -3192,7 +3497,7 @@ name: Sequence description
 namespace: operation
 def: "Retrieve basic information about a molecular sequence." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000004 ! Operation
-relationship: is_concern_of EDAM:0000155 ! Sequence retrieval
+relationship: is_concern_of EDAM:0000155 ! Sequence search and retrieval
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0002043 ! Sequence record lite
 
@@ -3254,7 +3559,7 @@ name: Sequence complexity calculation
 namespace: operation
 def: "Calculate sequence complexity, for example to find low-complexity regions in sequences." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000004 ! Operation
-relationship: is_concern_of EDAM:0000157 ! Sequence composition
+relationship: is_concern_of EDAM:0002263 ! Sequence complexity
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0001259 ! Sequence complexity
 
@@ -3285,7 +3590,7 @@ namespace: operation
 def: "Find or analyse repeat sequences in nucleotide sequences." [EDAM:EBI "EMBRACE definition"]
 comment: Repeat sequences include tandem repeats, inverted or palindromic repeats, DNA microsatellites (Simple Sequence Repeats or SSRs), interspersed repeats, maximal duplications and reverse, complemented and reverse complemented repeats etc. Repeat units can be exact or imperfect, in tandem or dispersed, of specified or unspecified length.
 is_a: EDAM:0000004 ! Operation
-relationship: is_concern_of EDAM:0000157 ! Sequence composition
+relationship: is_concern_of EDAM:0002262 ! Repeat sequences
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0001299 ! Repeat sequence report
 
@@ -3332,7 +3637,7 @@ namespace: operation
 def: "Analyse the sequence, conformational or physicochemical properties of transcription regulatory elements in DNA sequences." [EDAM:EBI "EMBRACE definition"]
 comment: For example transcription factor binding sites (TFBS) analysis to predict accessibility of DNA to binding factors.
 is_a: EDAM:0000004 ! Operation
-relationship: is_concern_of EDAM:0000110 ! Transcription regulatory sequence analysis
+relationship: is_concern_of EDAM:0000110 ! Transcription regulators
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000841 ! Undefined
 
@@ -3346,7 +3651,7 @@ namespace: operation
 def: "Calculate or extract a property of protein structure." [EDAM:EBI "EMBRACE definition"]
 comment: This might be a residue-level search for properties such as solvent accessibility, hydropathy, secondary structure, ligand-binding etc.
 is_a: EDAM:0000004 ! Operation
-relationship: is_concern_of EDAM:0000123 ! Protein physicochemical properties
+relationship: is_concern_of EDAM:0000123 ! Protein physicochemistry
 relationship: is_concern_of EDAM:0000126 ! Protein structure analysis
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0001537 ! Protein structure annotation
@@ -3374,7 +3679,7 @@ def: "Predict, identify or screen for 3D structural motifs in protein structure(
 comment: This includes conserved substructures and conserved geometry, such as spatial arrangement of secondary structure or protein backbone. Methods might use structure alignment, structural templates, searches for similar electrostatic potential and molecular surface shape, surface-mapping of phylogenetic information etc.
 synonym: "Protein structural feature identification" EXACT []
 is_a: EDAM:0000004 ! Operation
-relationship: is_concern_of EDAM:0000139 ! Protein structural features
+relationship: is_concern_of EDAM:0000166 ! Protein structural motifs
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000899 ! Protein 3D structural motif annotation
 
@@ -3418,7 +3723,7 @@ name: Torsion angle calculation
 namespace: operation
 def: "Calculate, visualise or analyse phi/psi angles of a protein structure." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000004 ! Operation
-relationship: is_concern_of EDAM:0000123 ! Protein physicochemical properties
+relationship: is_concern_of EDAM:0000123 ! Protein physicochemistry
 relationship: is_concern_of EDAM:0000126 ! Protein structure analysis
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000841 ! Undefined
@@ -3430,7 +3735,7 @@ name: Small molecule property calculation
 namespace: operation
 def: "Calculate or extract a physicochemical property of a small molecule." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000004 ! Operation
-relationship: is_concern_of EDAM:0000154 ! Small molecules analysis
+relationship: is_concern_of EDAM:0000154 ! Small molecules
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000841 ! Undefined
 
@@ -3440,7 +3745,7 @@ name: Protein physicochemical property calculation
 namespace: operation
 def: "Calculate or extract a physicochemical property of protein sequence(s)." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000004 ! Operation
-relationship: is_concern_of EDAM:0000123 ! Protein physicochemical properties
+relationship: is_concern_of EDAM:0000123 ! Protein physicochemistry
 relationship: is_concern_of EDAM:0000125 ! Protein sequence analysis
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000897 ! Protein physicochemical property
@@ -3452,7 +3757,7 @@ namespace: operation
 def: "Predict general functional properties of a protein." [EDAM:EBI "EMBRACE definition"]
 comment: For functional properties that can be mapped to a sequence, use 'Protein sequence feature detection' instead.
 is_a: EDAM:0000004 ! Operation
-relationship: is_concern_of EDAM:0001775 ! Protein function analysis
+relationship: is_concern_of EDAM:0002276 ! Protein function prediction
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0001776 ! Protein function annotation
 
@@ -3463,7 +3768,7 @@ name: Protein function comparison
 namespace: operation
 def: "Compare the general functional properties of two or more proteins." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000004 ! Operation
-relationship: is_concern_of EDAM:0001775 ! Protein function analysis
+relationship: is_concern_of EDAM:0001775 ! Protein function
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0001776 ! Protein function annotation
 
@@ -3476,7 +3781,7 @@ def: "Predict antigenicity (for example a Hopp and Woods plot), allergenicity /
 comment: This is usually done in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data.
 is_a: EDAM:0000004 ! Operation
 relationship: is_concern_of EDAM:0000125 ! Protein sequence analysis
-relationship: is_concern_of EDAM:0000201 ! Immunological analysis
+relationship: is_concern_of EDAM:0000201 ! Immunology
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0001534 ! Peptide immunogenicity report
 
@@ -3574,7 +3879,7 @@ name: Nucleic acid physicochemical property calculation
 namespace: operation
 def: "Calculate or extract a physicochemical property of nucleotide sequence(s)." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000004 ! Operation
-relationship: is_concern_of EDAM:0000094 ! Nucleic acid physicochemical properties
+relationship: is_concern_of EDAM:0000094 ! Nucleic acid physicochemistry
 relationship: is_concern_of EDAM:0000096 ! Nucleic acid sequence analysis
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000912 ! Nucleic acid physicochemical property
@@ -3585,8 +3890,8 @@ name: Nucleic acid structural property calculation
 namespace: operation
 def: "Calculate or extract a property of nucleic acid structure such as conformational parameters or properties." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000004 ! Operation
-relationship: is_concern_of EDAM:0000094 ! Nucleic acid physicochemical properties
-relationship: is_concern_of EDAM:0000077 ! Nucleic acid analysis
+relationship: is_concern_of EDAM:0000094 ! Nucleic acid physicochemistry
+relationship: is_concern_of EDAM:0000077 ! Nucleic acids
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000912 ! Nucleic acid physicochemical property
 
@@ -3611,7 +3916,7 @@ namespace: operation
 def: "Detect frameshift errors in DNA sequences (from sequencing projects)." [EDAM:EBI "EMBRACE definition"]
 comment: Methods include sequence alignment (if related sequences are available) and word-based sequence comparison.
 is_a: EDAM:0000004 ! Operation
-relationship: is_concern_of EDAM:0000102 ! Sequencing
+relationship: is_concern_of EDAM:0000102 ! Sequencing and mapping
 relationship: is_concern_of EDAM:0000159 ! Sequence comparison
 relationship: is_concern_of EDAM:0000096 ! Nucleic acid sequence analysis
 relationship: has_input EDAM:0000841 ! Undefined
@@ -3661,7 +3966,7 @@ name: Transmembrane protein prediction
 namespace: operation
 def: "Predict transmembrane proteins or transmembrane (helical) domains or regions in protein sequences." [EDAM:EBI  "EMBRACE definition"]
 is_a: EDAM:0000004 ! Operation
-relationship: is_concern_of EDAM:0000131 ! Transmembrane protein analysis
+relationship: is_concern_of EDAM:0000131 ! Transmembrane proteins
 relationship: is_concern_of EDAM:0000178 ! Protein secondary structure prediction
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0001456 ! Transmembrane protein secondary structure
@@ -3673,7 +3978,7 @@ namespace: operation
 def: "Analyse transmembrane proteins and domains / regions." [EDAM:EBI  "EMBRACE definition"]
 comment: Use this term for analysis of transmembrane domains (buried and exposed faces), transmembrane helices, helix topology, orientation, inter-helical contacts, membrane dipping (re-entrant) loops and other secondary structure etc. Methods might use pattern discovery, hidden Markov models, sequence alignment, structural profiles, amino acid property analysis, comparison to known domains or some combination (hybrid methods).
 is_a: EDAM:0000004 ! Operation
-relationship: is_concern_of EDAM:0000131 ! Transmembrane protein analysis
+relationship: is_concern_of EDAM:0000131 ! Transmembrane proteins
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0001456 ! Transmembrane protein secondary structure
 
@@ -3683,7 +3988,7 @@ name: Tertiary structure prediction
 namespace: operation
 def: "Predict tertiary structure of a molecular (biopolymer) sequence." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000004 ! Operation
-relationship: is_concern_of EDAM:0000171 ! Tertiary structure prediction
+relationship: is_concern_of EDAM:0000082 ! Structure prediction
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000883 ! Tertiary structure
 
@@ -3760,7 +4065,7 @@ namespace: operation
 def: "Predict RNA secondary structure (for example knots, pseudoknots, alternative structures etc)." [EDAM:EBI "EMBRACE definition"]
 comment: Methods might use RNA motifs, predicted intermolecular contacts, or RNA sequence-structure compatibility (inverse RNA folding).
 is_a: EDAM:0000004 ! Operation
-relationship: is_concern_of EDAM:0000181 ! RNA structure prediction
+relationship: is_concern_of EDAM:0000173 ! Nucleic acid structure prediction
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000880 ! RNA secondary structure
 
@@ -3976,7 +4281,7 @@ name: Sequence profile generation
 namespace: operation
 def: "Generate some type of sequence profile (for example a hidden Markov model) from a sequence alignment." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000004 ! Operation
-relationship: is_concern_of EDAM:0000188 ! Sequence profiles
+relationship: is_concern_of EDAM:0000188 ! Sequence profiles and HMMs
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0001354 ! Sequence profile
 
@@ -3998,7 +4303,7 @@ namespace: operation
 def: "Align sequence profiles (representing sequence alignments)." [EDAM:EBI "EMBRACE definition"]
 comment: See also 'Sequence alignment comparison'.
 is_a: EDAM:0000004 ! Operation
-relationship: is_concern_of EDAM:0000188 ! Sequence profiles
+relationship: is_concern_of EDAM:0000188 ! Sequence profiles and HMMs
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000868 ! Profile alignment
 
@@ -4022,7 +4327,7 @@ namespace: operation
 def: "Align molecular sequence(s) to sequence profile(s) (representing a sequence alignment)." [EDAM:EBI "EMBRACE definition"]
 comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons.
 is_a: EDAM:0000004 ! Operation
-relationship: is_concern_of EDAM:0000188 ! Sequence profiles
+relationship: is_concern_of EDAM:0000188 ! Sequence profiles and HMMs
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000869 ! Sequence-profile alignment
 
@@ -4033,11 +4338,11 @@ id: EDAM:0000302
 name: Sequence-structure alignment
 namespace: operation
 def: "Align molecular sequence to structure in 3D space (threading)." [EDAM:EBI "EMBRACE definition"]
-comment: Use this term for methods that evaluate sequence-structure compatibility by assessing residue interactions in 3D.  Methods might perform one-to-one, one-to-many or many-to-many comparisons.
+comment: Use this term for methods that evaluate sequence-structure compatibility by assessing residue interactions in 3D. Methods might perform one-to-one, one-to-many or many-to-many comparisons.
 synonym: "Threading" EXACT []
 is_a: EDAM:0000004 ! Operation
 relationship: is_concern_of EDAM:0000184 ! Sequence-structure alignment
-relationship: is_concern_of EDAM:0000175 ! Molecular modelling
+relationship: is_concern_of EDAM:0000175 ! Homology modelling
 relationship: is_concern_of EDAM:0000180 ! Protein fold recognition
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000893 ! Sequence-structure alignment
@@ -4048,8 +4353,8 @@ name: Protein fold recognition
 namespace: operation
 def: "Recognize (predict and assign) known protein structural domains or folds in protein sequence(s)." [EDAM:EBI "EMBRACE definition"]
 comment: Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH.
-synonym: "Protein domain prediction" EXACT [] 
-synonym: "Protein fold prediction" EXACT [] 
+synonym: "Protein domain prediction" EXACT []
+synonym: "Protein fold prediction" EXACT []
 is_a: EDAM:0000004 ! Operation
 relationship: is_concern_of EDAM:0000180 ! Protein fold recognition
 relationship: has_input EDAM:0000841 ! Undefined
@@ -4057,7 +4362,7 @@ relationship: has_output EDAM:0001564 ! Protein fold recognition report
 
 
 [Term]
-id: EDAM:0000304
+id: EDAM:0002246
 name: Demonstration
 namespace: operation
 def: "An operation performing purely illustrative (pedagogical) purposes." [EDAM:EBI "EMBRACE definition"]
@@ -4113,7 +4418,7 @@ id: EDAM:0000308
 name: PCR primer design
 namespace: operation
 def: "Design oligonucleotide primers for PCR and DNA amplification etc." [EDAM:EBI "EMBRACE definition"]
-comment: Primer design involves predicting or selecting primers that are specific to a provided PCR template.  Primers can be designed with certain properties such as size of product desired, primer size etc.  The output might be a minimal or overlapping primer set.
+comment: Primer design involves predicting or selecting primers that are specific to a provided PCR template. Primers can be designed with certain properties such as size of product desired, primer size etc. The output might be a minimal or overlapping primer set.
 is_a: EDAM:0000004 ! Operation
 relationship: is_concern_of EDAM:0000195 ! Polymerase chain reaction
 relationship: has_input EDAM:0000841 ! Undefined
@@ -4226,7 +4531,7 @@ namespace: operation
 def: "Analyse EST or cDNA sequences." [EDAM:EBI "EMBRACE definition"]
 comment: For example, identify full-length cDNAs from EST sequences or detect potential EST antisense transcripts.
 is_a: EDAM:0000004 ! Operation
-relationship: is_concern_of EDAM:0000205 ! EST and cDNA sequence analysis
+relationship: is_concern_of EDAM:0000197 ! Gene expression
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000841 ! Undefined
 
@@ -4275,7 +4580,7 @@ is_a: EDAM:0000004 ! Operation
 relationship: is_concern_of EDAM:0000172 ! Protein structure prediction
 relationship: is_concern_of EDAM:0000122 ! Structural genomics
 relationship: is_concern_of EDAM:0000126 ! Protein structure analysis
-relationship: is_concern_of EDAM:0000175 ! Molecular modelling
+relationship: is_concern_of EDAM:0000175 ! Homology modelling
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0001539 ! Protein structure evaluation
 
@@ -4285,13 +4590,13 @@ id: EDAM:0000322
 name: Protein tertiary structure refinement
 namespace: operation
 def: "Refine a model of protein structure to reduce steric clashes, volume irregularities etc." [EDAM:EBI "EMBRACE definition"]
-comment: The PDB file format has had difficulties, inconsistencies and errors.  Corrections can include identifying a meaningful sequence, removal of alternate atoms, correction of nomenclature problems, removal of incomplete residues and spurious waters, addition or removal of water, modelling of missing side chains, optimisation of cysteine bonds, regularisation of bond lengths, bond angles and planarities etc.
+comment: The PDB file format has had difficulties, inconsistencies and errors. Corrections can include identifying a meaningful sequence, removal of alternate atoms, correction of nomenclature problems, removal of incomplete residues and spurious waters, addition or removal of water, modelling of missing side chains, optimisation of cysteine bonds, regularisation of bond lengths, bond angles and planarities etc.
 xref: WHATIF: CorrectedPDBasXML
 is_a: EDAM:0000004 ! Operation
 relationship: is_concern_of EDAM:0000172 ! Protein structure prediction
 relationship: is_concern_of EDAM:0000122 ! Structural genomics
 relationship: is_concern_of EDAM:0000126 ! Protein structure analysis
-relationship: is_concern_of EDAM:0000175 ! Molecular modelling
+relationship: is_concern_of EDAM:0000175 ! Homology modelling
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0001460 ! Protein tertiary structure
 
@@ -4380,7 +4685,7 @@ name: Protein SNP mapping
 namespace: operation
 def: "Map single nucleotide polymorphisms (SNPs) on protein structure(s)." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000004 ! Operation
-relationship: is_concern_of EDAM:0000199 ! Mutation and polymorphism
+relationship: is_concern_of EDAM:0002277 ! SNPs
 relationship: is_concern_of EDAM:0000126 ! Protein structure analysis
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000841 ! Undefined
@@ -4404,7 +4709,7 @@ name: Immunogen design
 namespace: operation
 def: "Design molecules that elicit an immune response (immunogens)." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000004 ! Operation
-relationship: is_concern_of EDAM:0000201 ! Immunological analysis
+relationship: is_concern_of EDAM:0000201 ! Immunology
 relationship: is_concern_of EDAM:0000150 ! Protein rational design
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000841 ! Undefined
@@ -4498,7 +4803,7 @@ relationship: has_output EDAM:0000841 ! Undefined
 id: EDAM:0000336
 name: File debugging
 namespace: operation
-def: "Debug or test a file." [EDAM:EBI "EMBRACE definition"]
+def: "Debug, test or validate a file." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000004 ! Operation
 relationship: is_concern_of EDAM:0000220 ! File handling
 relationship: has_input EDAM:0000841 ! Undefined
@@ -4531,7 +4836,7 @@ namespace: operation
 def: "Query a sequence database and retrieve sequences." [EDAM:EBI "EMBRACE definition"]
 comment: This includes direct retrieval methods (e.g. the dbfetch program) but not those that perform calculations on the sequence.
 is_a: EDAM:0000224 ! Database search and retrieval
-relationship: is_concern_of EDAM:0000155 ! Sequence retrieval
+relationship: is_concern_of EDAM:0000155 ! Sequence search and retrieval
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000849 ! Sequence record
 
@@ -4555,7 +4860,7 @@ comment: This includes direct retrieval methods but not those that perform calcu
 xref: WHATIF:DownloadPDB
 xref: WHATIF:EchoPDB
 is_a: EDAM:0000224 ! Database search and retrieval
-relationship: is_concern_of EDAM:0000165 ! Structure retrieval
+relationship: is_concern_of EDAM:0000165 ! Structure search and retrieval
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000883 ! Tertiary structure
 
@@ -4598,7 +4903,7 @@ namespace: operation
 def: "Query a profile database and retrieve one or more profile(s)." [EDAM:EBI "EMBRACE definition"]
 comment: This includes direct retrieval methods that retrieve a profile by, e.g. the profile name.
 is_a: EDAM:0000224 ! Database search and retrieval
-relationship: is_concern_of EDAM:0000188 ! Sequence profiles
+relationship: is_concern_of EDAM:0000188 ! Sequence profiles and HMMs
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000849 ! Sequence record
 
@@ -4609,7 +4914,7 @@ namespace: operation
 def: "Search a database of sequence profiles with a query sequence." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000224 ! Database search and retrieval
 is_a: EDAM:0000300 ! Sequence-profile alignment
-relationship: is_concern_of EDAM:0000188 ! Sequence profiles
+relationship: is_concern_of EDAM:0000188 ! Sequence profiles and HMMs
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000869 ! Sequence-profile alignment
 relationship: has_output EDAM:0001298 ! Sequence motif report
@@ -4621,23 +4926,42 @@ name: Transmembrane protein database search
 namespace: operation
 def: "Search a database of transmembrane proteins, for example for sequence or structural similarities." [EDAM:EBI  "EMBRACE definition"]
 is_a: EDAM:0000224 ! Database search and retrieval
-relationship: is_concern_of EDAM:0000131 ! Transmembrane protein analysis
+relationship: is_concern_of EDAM:0000131 ! Transmembrane proteins
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000841 ! Undefined
 
 
+[Term]
+id: EDAM:0002264
+name: Pathway retrieval
+namespace: operation
+def: "Query a biological pathways database and retrieve one or more pathways." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0000224 ! Database search and retrieval
+relationship: is_concern_of EDAM:0000198 ! Biological pathways
+relationship: has_input EDAM:0000841 ! Undefined
+relationship: has_output EDAM:0000946 ! Biological pathway
 
 
-!
-! Operation<-Database search and retrieval<-Sequence retrieval
-!
 [Term]
-id: EDAM:0000344
-name: Sequence retrieval by code
+id: EDAM:0002265
+name: Identifier retrieval
+namespace: operation
+def: "Query a database and retrieve one or more data identifiers." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0000224 ! Database search and retrieval
+relationship: is_concern_of EDAM:0000090 ! Database search and retrieval
+relationship: has_input EDAM:0000841 ! Undefined
+relationship: has_output EDAM:0000842 ! Identifier
+
+!
+! Operation<-Database search and retrieval<-Sequence retrieval
+!
+[Term]
+id: EDAM:0000344
+name: Sequence retrieval by code
 namespace: operation
 def: "Query a database and retrieve sequences with a given entry code or accession number." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0001813 ! Sequence retrieval
-relationship: is_concern_of EDAM:0001813 ! Sequence retrieval
+relationship: is_concern_of EDAM:0001813 ! Sequence search and retrieval
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000849 ! Sequence record
 
@@ -4647,11 +4971,12 @@ name: Sequence retrieval by keyword
 namespace: operation
 def: "Query a database and retrieve sequences containing a given keyword." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0001813 ! Sequence retrieval
-relationship: is_concern_of EDAM:0001813 ! Sequence retrieval
+relationship: is_concern_of EDAM:0001813 ! Sequence search and retrieval
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000849 ! Sequence record
 
 
+
 !
 ! Operation<-Database search and retrieval<-Sequence retrieval<-Sequence retrieval by code
 !
@@ -4662,7 +4987,7 @@ namespace: operation
 def: "Extract a molecular sequence from a PDB file." [EDAM:WHATIF "EMBRACE definition"]
 xref: WHATIF: PDB_sequence
 is_a: EDAM:0000344 ! Sequence retrieval by code
-relationship: is_concern_of EDAM:0000076 ! Undefined
+relationship: is_concern_of EDAM:0001813 ! Sequence search and retrieval
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000841 ! Undefined
 
@@ -4679,7 +5004,7 @@ namespace: operation
 def: "Search a sequence database and retrieve sequences that are similar to a query sequence." [EDAM:EBI "EMBRACE definition"]
 synonym: "Sequence similarity search" EXACT []
 is_a: EDAM:0000338 ! Sequence database search
-relationship: is_concern_of EDAM:0000159 ! Sequence comparison
+relationship: is_concern_of EDAM:0000163 ! Sequence similarity search
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000857 ! Sequence database hits
 
@@ -4691,7 +5016,7 @@ namespace: operation
 def: "Search a sequence database and retrieve sequences matching a given sequence motif or pattern, such as a Prosite pattern or regular expression." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000338 ! Sequence database search
 is_a: EDAM:0000239 ! Sequence motif searching
-relationship: is_concern_of EDAM:0000159 ! Sequence comparison
+relationship: is_concern_of EDAM:0000163 ! Sequence similarity search
 relationship: is_concern_of EDAM:0000158 ! Sequence motifs
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000849 ! Sequence record
@@ -4704,7 +5029,7 @@ namespace: operation
 def: "Search a sequence database and retrieve sequences of a given amino acid composition." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000338 ! Sequence database search
 relationship: is_concern_of EDAM:0000157 ! Sequence composition
-relationship: is_concern_of EDAM:0000159 ! Sequence comparison
+relationship: is_concern_of EDAM:0000163 ! Sequence similarity search
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000849 ! Sequence record
 
@@ -4714,17 +5039,11 @@ name: Sequence database search by physicochemical property
 namespace: operation
 def: "Search a sequence database and retrieve sequences with a specified physicochemical property." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000338 ! Sequence database search
-relationship: is_concern_of EDAM:0000159 ! Sequence comparison
+relationship: is_concern_of EDAM:0000163 ! Sequence similarity search
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000849 ! Sequence record
 
-!
-! Operation<-Database search and retrieval<-Sequence database search<-Sequence database search by code
-!
 
-!
-! Operation<-Database search and retrieval<-Sequence database search<-Sequence database search by keyword
-!
 
 !
 ! Operation<-Database search and retrieval<-Sequence database search<-Sequence database search by sequence
@@ -4738,7 +5057,7 @@ comment: Word-based methods (for example BLAST, gapped BLAST, MEGABLAST, WU-BLAS
 synonym: "Sequence similarity search (word-based methods)" EXACT []
 is_a: EDAM:0000346 ! Sequence database search by sequence
 is_a: EDAM:0000288 ! Sequence word comparison
-relationship: is_concern_of EDAM:0000159 ! Sequence comparison
+relationship: is_concern_of EDAM:0000163 ! Sequence similarity search
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000857 ! Sequence database hits
 
@@ -4751,8 +5070,8 @@ comment: This includes tools based on PSI-BLAST.
 synonym: "Sequence similarity search (profile-based methods)" EXACT []
 is_a: EDAM:0000346 ! Sequence database search by sequence
 is_a: EDAM:0000300 ! Sequence-profile alignment
-relationship: is_concern_of EDAM:0000159 ! Sequence comparison
-relationship: is_concern_of EDAM:0000188 ! Sequence profiles
+relationship: is_concern_of EDAM:0000163 ! Sequence similarity search
+relationship: is_concern_of EDAM:0000188 ! Sequence profiles and HMMs
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000857 ! Sequence database hits
 
@@ -4765,6 +5084,7 @@ comment: This includes tools based on the Smith-Waterman algorithm or FASTA.
 synonym: "Sequence similarity search (local alignment-based methods) " EXACT []
 is_a: EDAM:0000346 ! Sequence database search by sequence
 is_a: EDAM:0000292 ! Sequence alignment
+relationship: is_concern_of EDAM:0000163 ! Sequence similarity search
 relationship: is_concern_of EDAM:0000182 ! Sequence alignment
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000857 ! Sequence database hits
@@ -4778,6 +5098,7 @@ comment: This includes tools based on the Needleman and Wunsch algorithm.
 synonym: "Sequence similarity search (global alignment-based methods)" EXACT []
 is_a: EDAM:0000346 ! Sequence database search by sequence
 is_a: EDAM:0000292 ! Sequence alignment
+relationship: is_concern_of EDAM:0000163 ! Sequence similarity search
 relationship: is_concern_of EDAM:0000182 ! Sequence alignment
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000857 ! Sequence database hits
@@ -4790,7 +5111,7 @@ def: "Search a DNA database (for example a database of conserved sequence tags)
 comment: STSs are genetic markers that are easily detected by the polymerase chain reaction (PCR) using specific primers.
 synonym: "Sequence similarity search (primer sequences)" EXACT []
 is_a: EDAM:0000346 ! Sequence database search by sequence
-relationship: is_concern_of EDAM:0000159 ! Sequence comparison
+relationship: is_concern_of EDAM:0000163 ! Sequence similarity search
 relationship: is_concern_of EDAM:0000195 ! Polymerase chain reaction
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000857 ! Sequence database hits
@@ -4822,7 +5143,7 @@ synonym: "Protein fingerprinting" EXACT []
 synonym: "Peptide mass fingerprinting" EXACT []
 is_a: EDAM:0000349 ! Sequence database search by physicochemical property
 relationship: is_concern_of EDAM:0000141 ! Proteolysis and peptide mass
-relationship: is_concern_of EDAM:0000123 ! Protein physicochemical properties
+relationship: is_concern_of EDAM:0000123 ! Protein physicochemistry
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000849 ! Sequence record
 
@@ -4833,7 +5154,7 @@ name: Sequence database search by isoelectric point
 namespace: operation
 def: "Search sequence(s) or a sequence database for sequences of a given isoelectric point." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000349 ! Sequence database search by physicochemical property
-relationship: is_concern_of EDAM:0000123 ! Protein physicochemical properties
+relationship: is_concern_of EDAM:0000123 ! Protein physicochemistry
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000849 ! Sequence record
 
@@ -4848,7 +5169,7 @@ name: Structure retrieval by code
 namespace: operation
 def: "Query a tertiary structure database and retrieve entries with a given entry code or accession number." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000339 ! Structure retrieval
-relationship: is_concern_of EDAM:0001814 ! Structure retrieval
+relationship: is_concern_of EDAM:0001814 ! Structure search and retrieval
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000883 ! Tertiary structure
 
@@ -4858,8 +5179,7 @@ name: Structure retrieval by keyword
 namespace: operation
 def: "Query a tertiary structure database and retrieve entries containing a given keyword." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000339 ! Structure retrieval
-relationship: is_concern_of EDAM:0001814 ! Structure retrieval
-relationship: is_concern_of EDAM:0000165 ! Structure retrieval
+relationship: is_concern_of EDAM:0000165 ! Structure search and retrieval
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000883 ! Tertiary structure
 
@@ -4870,7 +5190,7 @@ namespace: operation
 def: "Query a tertiary structure database and retrieve water molecules." [EDAM:EBI "EMBRACE definition"]
 xref: WHATIF:MovedWaterPDB
 is_a: EDAM:0000224 ! Database search and retrieval
-relationship: is_concern_of EDAM:0000165 ! Structure retrieval
+relationship: is_concern_of EDAM:0000165 ! Structure search and retrieval
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000883 ! Tertiary structure
 
@@ -5121,7 +5441,7 @@ name: Protein sequence complexity calculation
 namespace: operation
 def: "Calculate protein sequence complexity." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000234 ! Sequence complexity calculation
-relationship: is_concern_of EDAM:0000125 ! Protein sequence analysis
+relationship: is_concern_of EDAM:0002263 ! Sequence complexity
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0001259 ! Sequence complexity
 
@@ -5131,7 +5451,7 @@ name: Nucleotide sequence complexity calculation
 namespace: operation
 def: "Calculate nucleotide sequence complexity, for example to find low-complexity regions in sequences." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000234 ! Sequence complexity calculation
-relationship: is_concern_of EDAM:0000096 ! Nucleic acid sequence analysis
+relationship: is_concern_of EDAM:0002263 ! Sequence complexity
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0001259 ! Sequence complexity
 
@@ -5183,6 +5503,23 @@ relationship: is_concern_of EDAM:0000125 ! Protein sequence analysis
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0001261 ! Sequence composition
 
+
+!
+! Operation<-Sequence composition analysis<-Nucleotide base composition analysis
+!
+[Term]
+id: EDAM:0002284
+name: Nucleic acid density plot calculation
+namespace: operation
+def: "Calculate a density plot (of base composition) for a nucleotide sequence." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0000377 ! Nucleotide base composition analysis
+relationship: is_concern_of EDAM:0000096 ! Nucleic acid sequence analysis
+relationship: is_concern_of EDAM:0000157 ! Sequence composition
+relationship: has_input EDAM:0000841 ! Undefined
+relationship: has_output EDAM:0001261 ! Sequence composition
+
+
+
 !
 ! Operation<-Repeat sequence analysis
 !
@@ -5192,7 +5529,7 @@ name: Repeat sequence identification
 namespace: operation
 def: "Find short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000237 ! Repeat sequence analysis
-relationship: is_concern_of EDAM:0000157 ! Sequence composition
+relationship: is_concern_of EDAM:0002262 ! Repeat sequences
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0001299 ! Repeat sequence report
 
@@ -5202,7 +5539,7 @@ name: Repeat sequence organisation analysis
 namespace: operation
 def: "Analyse or visualise repeat sequence organization, periodicity etc." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000237 ! Repeat sequence analysis
-relationship: is_concern_of EDAM:0000157 ! Sequence composition
+relationship: is_concern_of EDAM:0002262 ! Repeat sequences
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0001299 ! Repeat sequence report
 
@@ -5247,9 +5584,9 @@ id: EDAM:0000242
 name: Transcription regulatory sequence comparative analysis
 namespace: operation
 def: "Identify common, conserved (homologous) or synonymous transcriptional regulatory motifs." [EDAM:EBI "EMBRACE definition"]
-comment: For example cross-species comparison of transcription factor binding sites (TFBS).  Methods might analyse co-regulated or co-expressed genes, or sets of oppositely expressed genes.
+comment: For example cross-species comparison of transcription factor binding sites (TFBS). Methods might analyse co-regulated or co-expressed genes, or sets of oppositely expressed genes.
 is_a: EDAM:0000241 ! Transcription regulatory sequence analysis
-relationship: is_concern_of EDAM:0000110 ! Transcription regulatory sequence analysis
+relationship: is_concern_of EDAM:0000110 ! Transcription regulators
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000841 ! Undefined
 
@@ -5281,7 +5618,7 @@ namespace: operation
 def: "Calculate solvent accessible or buried surface areas in protein structures." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000243 ! Protein structural property calculation
 relationship: is_concern_of EDAM:0000137 ! Protein hydropathy
-relationship: is_concern_of EDAM:0000146 ! Protein surface analysis
+relationship: is_concern_of EDAM:0000146 ! Protein surfaces
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0001542 ! Protein solvent accessibility
 
@@ -5330,7 +5667,7 @@ name: Protein surface and interior calculation
 namespace: operation
 def: "Identify the protein surface and interior, surface accessible pockets, interior inaccessible cavities etc." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000384 ! Protein solvent accessibility calculation
-relationship: is_concern_of EDAM:0000146 ! Protein surface analysis
+relationship: is_concern_of EDAM:0000146 ! Protein surfaces
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0001543 ! Protein surface
 
@@ -5396,7 +5733,7 @@ relationship: has_output EDAM:0000841 ! Undefined
 id: EDAM:0001820
 name: Protein residue vacuum accessible surface calculation
 namespace: operation
-def: "Calculate the solvent accessibility ('vacuum accessible surface') for each residue in a structure.  This is the accessibility of the residue when taken out of the protein together with the the backbone atoms of any residue it is covalently bound to." [EDAM:WHATIF "EMBRACE definition"]
+def: "Calculate the solvent accessibility ('vacuum accessible surface') for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the the backbone atoms of any residue it is covalently bound to." [EDAM:WHATIF "EMBRACE definition"]
 comment: Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain).
 xref: WHATIF:ResidueAccessibilityVacuum
 is_a: EDAM:0000387 ! Protein surface and interior calculation
@@ -5423,7 +5760,7 @@ relationship: has_output EDAM:0000841 ! Undefined
 id: EDAM:0001822
 name: Protein residue vacuum molecular surface calculation
 namespace: operation
-def: "Calculate the solvent accessibility ('vacuum molecular surface') for each residue in a structure.  This is the accessibility of the residue when taken out of the protein together with the the backbone atoms of any residue it is covalently bound to." [EDAM:WHATIF "EMBRACE definition"]
+def: "Calculate the solvent accessibility ('vacuum molecular surface') for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the the backbone atoms of any residue it is covalently bound to." [EDAM:WHATIF "EMBRACE definition"]
 comment: Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain).
 xref: WHATIF:ResidueAccessibilityVacuumMolecular
 is_a: EDAM:0000387 ! Protein surface and interior calculation
@@ -5602,7 +5939,7 @@ id: EDAM:0001839
 name: Salt bridge identification
 namespace: operation
 def: "Identify (and possibly score) salt bridges in a protein structure." [EDAM:WHATIF "EMBRACE definition"]
-comment: Salt bridges are interactions between oppositely charged atoms in different residues.  The output might include the inter-atomic distance.
+comment: Salt bridges are interactions between oppositely charged atoms in different residues. The output might include the inter-atomic distance.
 xref: WHATIF:HasSaltBridge
 xref: WHATIF:HasSaltBridgePlus
 xref: WHATIF:ShowSaltBridges
@@ -5617,7 +5954,7 @@ id: EDAM:0001846
 name: HET group identification
 namespace: operation
 def: "Identify HET groups in PDB files." [EDAM:WHATIF "EMBRACE definition"]
-comment: A HET group usually corresponds to ligands, lipids, but might also (not consistently) include groups that are attached to amino acids.  Each HET group is supposed to have a unique three letter code and a unique name which might be given in the output.
+comment: A HET group usually corresponds to ligands, lipids, but might also (not consistently) include groups that are attached to amino acids. Each HET group is supposed to have a unique three letter code and a unique name which might be given in the output.
 xref: WHATIF: HETGroupNames
 is_a: EDAM:0000248 ! Protein residue interaction analysis
 relationship: is_concern_of EDAM:0000076 ! Undefined
@@ -5830,7 +6167,7 @@ name: Protein extinction coefficient calculation
 namespace: operation
 def: "Predict extinction coefficients or optical density of a protein sequence." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000250 ! Protein physicochemical property calculation
-relationship: is_concern_of EDAM:0000123 ! Protein physicochemical properties
+relationship: is_concern_of EDAM:0000123 ! Protein physicochemistry
 relationship: is_concern_of EDAM:0000125 ! Protein sequence analysis
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000897 ! Protein physicochemical property
@@ -5990,7 +6327,7 @@ namespace: operation
 def: "Predict MHC class I or class II binding peptides, promiscuous binding peptides, immunogenicity etc." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000252 ! Peptide immunogenicity prediction
 relationship: is_concern_of EDAM:0000125 ! Protein sequence analysis
-relationship: is_concern_of EDAM:0000201 ! Immunological analysis
+relationship: is_concern_of EDAM:0000201 ! Immunology
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000841 ! Undefined
 
@@ -6008,7 +6345,7 @@ namespace: operation
 def: "Identify or predict features in protein sequences such as functional sites or regions." [EDAM:EBI "EMBRACE definition"]
 comment: Methods might use protein sequence alignments, linear motifs and patterns.
 is_a: EDAM:0000253 ! Sequence feature detection
-relationship: is_concern_of EDAM:0000138 ! Protein sequence features
+relationship: is_concern_of EDAM:0000124 ! Protein features
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0001271 ! Sequence feature report
 
@@ -6019,7 +6356,7 @@ namespace: operation
 def: "Identify or predict features in nucleotide sequences such as functional sites or regions." [EDAM:EBI "EMBRACE definition"]
 comment: Methods might use protein sequence alignments, linear motifs and patterns.
 is_a: EDAM:0000253 ! Sequence feature detection
-relationship: is_concern_of EDAM:0000105 ! Nucleic acid sequence features
+relationship: is_concern_of EDAM:0000095 ! Nucleic acid features
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0001271 ! Sequence feature report
 
@@ -6034,7 +6371,7 @@ namespace: operation
 def: "Identify or predict antigenic determinant sites (epitopes) in protein sequences." [EDAM:EBI "EMBRACE definition"]
 comment: Epitope mapping is commonly done during vaccine design.
 is_a: EDAM:0000414 ! Protein sequence feature detection
-relationship: is_concern_of EDAM:0000201 ! Immunological analysis
+relationship: is_concern_of EDAM:0000201 ! Immunology
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0001271 ! Sequence feature report
 
@@ -6054,7 +6391,7 @@ id: EDAM:0000418
 name: Protein signal peptide identification
 namespace: operation
 def: "Identify signal peptides and signal peptide cleavage sites in protein sequences." [EDAM:EBI "EMBRACE definition"]
-comment: This can be used to predict subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or export (extracellular proteins) of a protein.  Methods might use sequence motifs and features, amino acid composition, profiles, machine-learned classifiers, etc.
+comment: This can be used to predict subcellular localization (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or export (extracellular proteins) of a protein. Methods might use sequence motifs and features, amino acid composition, profiles, machine-learned classifiers, etc.
 synonym: "Protein targeting prediction" EXACT []
 is_a: EDAM:0000414 ! Protein sequence feature detection
 relationship: is_concern_of EDAM:0000140 ! Protein targeting
@@ -6114,7 +6451,7 @@ name: MHC Class I epitope mapping
 namespace: operation
 def: "Predict epitopes that bind to MHC class I molecules." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000416 ! Epitope mapping
-relationship: is_concern_of EDAM:0000201 ! Immunological analysis
+relationship: is_concern_of EDAM:0000201 ! Immunology
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0001271 ! Sequence feature report
 
@@ -6125,7 +6462,7 @@ name: MHC Class II epitope mapping
 namespace: operation
 def: "Predict epitopes that bind to MHC class II molecules." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000416 ! Epitope mapping
-relationship: is_concern_of EDAM:0000201 ! Immunological analysis
+relationship: is_concern_of EDAM:0000201 ! Immunology
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0001271 ! Sequence feature report
 
@@ -6212,7 +6549,7 @@ name: Transposon prediction
 namespace: operation
 def: "Identify or predict transposons, retrotransposons / retrotransposition signatures etc." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000415 ! Nucleic acid sequence feature detection
-relationship: is_concern_of EDAM:0000105 ! Nucleic acid sequence features
+relationship: is_concern_of EDAM:0000095 ! Nucleic acid features
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0001301 ! Transposon report
 
@@ -6222,7 +6559,7 @@ name: PolyA signal identification
 namespace: operation
 def: "Identify polyA signals in nucleotide sequences." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000415 ! Nucleic acid sequence feature detection
-relationship: is_concern_of EDAM:0000105 ! Nucleic acid sequence features
+relationship: is_concern_of EDAM:0000095 ! Nucleic acid features
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0001302 ! PolyA signal report
 
@@ -6233,7 +6570,7 @@ namespace: operation
 def: "Identify quadruplex-forming motifs and predict quadruplex structures in nucleotide sequences." [EDAM:EBI "EMBRACE definition"]
 comment: Quadruplex structures are formed by guanine-rich regions and are implicated in various important biological processes and as therapeutic targets.
 is_a: EDAM:0000415 ! Nucleic acid sequence feature detection
-relationship: is_concern_of EDAM:0000105 ! Nucleic acid sequence features
+relationship: is_concern_of EDAM:0000095 ! Nucleic acid features
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0001271 ! Sequence feature report
 
@@ -6242,7 +6579,7 @@ id: EDAM:0000430
 name: CpG island and isochores identification
 namespace: operation
 def: "Identify and analyse CpG rich regions in a nucleotide sequence or isochores in genome sequences." [EDAM:EBI "EMBRACE definition"]
-comment: An isochore is long region (> 3 KB) of DNA with very uniform GC content, in contrast to the rest of the genome. Isochores tend tends to have more genes, higher local melting or denaturation temperatures, and different flexibility.  Methods might calculate fractional GC content or variation of GC content, predict methylation status of CpG islands etc.
+comment: An isochore is long region (> 3 KB) of DNA with very uniform GC content, in contrast to the rest of the genome. Isochores tend tends to have more genes, higher local melting or denaturation temperatures, and different flexibility. Methods might calculate fractional GC content or variation of GC content, predict methylation status of CpG islands etc.
 is_a: EDAM:0000415 ! Nucleic acid sequence feature detection
 relationship: is_concern_of EDAM:0000157 ! Sequence composition
 relationship: has_input EDAM:0000841 ! Undefined
@@ -6304,7 +6641,7 @@ name: tRNA identification
 namespace: operation
 def: "Identify or predict tRNA genes in genomic sequences (tRNA)." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000425 ! Gene prediction
-relationship: is_concern_of EDAM:0000115 ! tRNA analysis
+relationship: is_concern_of EDAM:0000115 ! tRNA
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000841 ! Undefined
 
@@ -6342,7 +6679,7 @@ namespace: operation
 def: "Identify or predict transcription regulatory motifs, patterns, elements or regions in DNA sequences." [EDAM:EBI "EMBRACE definition"]
 comment: This includes promoters, enhancers, silencers and boundary elements / insulators, regulatory protein or transcription factor binding sites etc. Methods might be specific to a particular genome and use motifs, word-based / grammatical methods, position-specific frequency matrices, discriminative pattern analysis etc.
 is_a: EDAM:0000426 ! Gene structure prediction
-relationship: is_concern_of EDAM:0000110 ! Transcription regulatory sequence analysis
+relationship: is_concern_of EDAM:0000110 ! Transcription regulators
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0001271 ! Sequence feature report
 
@@ -6386,7 +6723,7 @@ namespace: operation
 def: "Identify, predict or analyse cis-regulatory elements (TATA box, Pribnow box, SOS box, CAAT box, CCAAT box, operator etc.) in DNA sequences." [EDAM:EBI "EMBRACE definition"]
 comment: Cis-regulatory elements (cis-elements) regulate the expression of genes located on the same strand. Cis-elements are found in the 5' promoter region of the gene, in an intron, or in the 3' untranslated region. Cis-elements are often binding sites of one or more trans-acting factors.
 is_a: EDAM:0000438 ! Transcription regulatory sequence prediction
-relationship: is_concern_of EDAM:0000110 ! Transcription regulatory sequence analysis
+relationship: is_concern_of EDAM:0000110 ! Transcription regulators
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0001271 ! Sequence feature report
 
@@ -6398,7 +6735,7 @@ namespace: operation
 def: "Identify, predict or analyse cis-regulatory elements (for example riboswitches) in RNA sequences." [EDAM:EBI "EMBRACE definition"]
 comment: Cis-regulatory elements (cis-elements) regulate genes located on the same strand from which the element was transcribed. A riboswitch is a region of an mRNA molecule that bind a small target molecule that regulates the gene's activity.
 is_a: EDAM:0000438 ! Transcription regulatory sequence prediction
-relationship: is_concern_of EDAM:0000110 ! Transcription regulatory sequence analysis
+relationship: is_concern_of EDAM:0000110 ! Transcription regulators
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0001271 ! Sequence feature report
 
@@ -6411,8 +6748,8 @@ def: "Identify or predict functional RNA sequences with a gene regulatory role (
 comment: Trans-regulatory elements regulate genes distant from the gene from which they were transcribed.
 synonym: "Functional RNA identification" EXACT []
 is_a: EDAM:0000438 ! Transcription regulatory sequence prediction
-relationship: is_concern_of EDAM:0000110 ! Transcription regulatory sequence analysis
-relationship: is_concern_of EDAM:0000113 ! Functional RNA analysis
+relationship: is_concern_of EDAM:0000110 ! Transcription regulators
+relationship: is_concern_of EDAM:0000113 ! Functional RNA
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0001271 ! Sequence feature report
 
@@ -6425,7 +6762,7 @@ namespace: operation
 def: "Identify matrix/scaffold attachment regions (MARs/SARs) in DNA sequences." [EDAM:EBI "EMBRACE definition"]
 comment: MAR/SAR sites often flank a gene or gene cluster and are found nearby cis-regulatory sequences. They might contribute to transcription regulation.
 is_a: EDAM:0000438 ! Transcription regulatory sequence prediction
-relationship: is_concern_of EDAM:0000110 ! Transcription regulatory sequence analysis
+relationship: is_concern_of EDAM:0000110 ! Transcription regulators
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0001308 ! Matrix/scaffold attachment site report
 
@@ -6475,7 +6812,7 @@ name: siRNA duplex identification
 namespace: operation
 def: "Identify or predict siRNA duplexes in RNA." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000443 ! Trans-regulatory element prediction
-relationship: is_concern_of EDAM:0000118 ! siRNA analysis
+relationship: is_concern_of EDAM:0000118 ! siRNA
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000841 ! Undefined
 
@@ -6486,7 +6823,7 @@ name: siRNA assay design
 namespace: operation
 def: "Design an siRNA sequence and assess binding specificity, for example for a functional assay." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000443 ! Trans-regulatory element prediction
-relationship: is_concern_of EDAM:0000118 ! siRNA analysis
+relationship: is_concern_of EDAM:0000118 ! siRNA
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000841 ! Undefined
 
@@ -6497,7 +6834,7 @@ name: microRNA identification
 namespace: operation
 def: "Identify or predict microRNA sequences (miRNA) and precursors or microRNA targets / binding sites in an RNA sequence." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000443 ! Trans-regulatory element prediction
-relationship: is_concern_of EDAM:0000117 ! microRNA analysis
+relationship: is_concern_of EDAM:0000117 ! microRNA
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0001310 ! microRNA report
 
@@ -6618,7 +6955,7 @@ name: Nucleosome formation potential prediction
 namespace: operation
 def: "Predict nucleosome formation potential of DNA sequences." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000261 ! Nucleic acid physicochemical property calculation
-relationship: is_concern_of EDAM:0000094 ! Nucleic acid physicochemical properties
+relationship: is_concern_of EDAM:0000094 ! Nucleic acid physicochemistry
 relationship: is_concern_of EDAM:0000096 ! Nucleic acid sequence analysis
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000912 ! Nucleosome exclusion sequence report
@@ -6661,7 +6998,7 @@ name: Nucleosome exclusion sequence prediction
 namespace: operation
 def: "Identify or predict nucleosome exclusion sequences (nucleosome free regions) in DNA." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000453 ! Nucleosome formation potential prediction
-relationship: is_concern_of EDAM:0000094 ! Nucleic acid physicochemical properties
+relationship: is_concern_of EDAM:0000094 ! Nucleic acid physicochemistry
 relationship: is_concern_of EDAM:0000096 ! Nucleic acid sequence analysis
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0001306 ! Nucleosome exclusion sequence report
@@ -6736,7 +7073,7 @@ def: "Calculate curvature and flexibility / stiffness of a nuclotide sequence."
 comment: This includes properties such as.
 is_a: EDAM:0000262 ! Nucleic acid structural property calculation
 relationship: is_concern_of EDAM:0000096 ! Nucleic acid sequence analysis
-relationship: is_concern_of EDAM:0000094 ! Nucleic acid physicochemical properties
+relationship: is_concern_of EDAM:0000094 ! Nucleic acid physicochemistry
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000912 ! Nucleic acid physicochemical property
 
@@ -6843,7 +7180,7 @@ name: G protein-coupled receptor (GPCR) prediction
 namespace: operation
 def: "Predict G protein-coupled receptors (GPCR)" [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000269 ! Transmembrane protein prediction
-relationship: is_concern_of EDAM:0000151 ! G protein-coupled receptor (GPCR) analysis
+relationship: is_concern_of EDAM:0000151 ! G protein-coupled receptors (GPCR)
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000841 ! Undefined
 
@@ -6864,7 +7201,7 @@ name: G protein-coupled receptor (GPCR) analysis and classification
 namespace: operation
 def: "Predict GPCR-G-protein coupling selectivity and classify G-protein coupled receptors (GPCRs) into families and subfamilies" [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000270 ! Transmembrane protein analysis
-relationship: is_concern_of EDAM:0000151 ! G protein-coupled receptor (GPCR) analysis
+relationship: is_concern_of EDAM:0000151 ! G protein-coupled receptors (GPCR)
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000841 ! Undefined
 
@@ -6916,7 +7253,7 @@ namespace: operation
 def: "Build a three-dimensional protein model based on known (for example homologues) structures (homology modelling)." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000474 ! Protein tertiary structure prediction
 relationship: is_concern_of EDAM:0000179 ! Protein tertiary structure prediction
-relationship: is_concern_of EDAM:0000175 ! Molecular modelling
+relationship: is_concern_of EDAM:0000175 ! Homology modelling
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000883 ! Tertiary structure
 
@@ -6953,7 +7290,7 @@ def: "Model protein backbone conformation." [EDAM:EBI "EMBRACE definition"]
 comment: Methods might require a preliminary C(alpha) trace.
 is_a: EDAM:0000477 ! Protein structure comparative modelling
 relationship: is_concern_of EDAM:0000179 ! Protein tertiary structure prediction
-relationship: is_concern_of EDAM:0000175 ! Molecular modelling
+relationship: is_concern_of EDAM:0000175 ! Homology modelling
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000883 ! Tertiary structure
 
@@ -6965,7 +7302,7 @@ def: "Model, analyse or edit amino acid side chain conformation in protein struc
 comment: Methods might use a residue rotamer library.
 is_a: EDAM:0000477 ! Protein structure comparative modelling
 relationship: is_concern_of EDAM:0000179 ! Protein tertiary structure prediction
-relationship: is_concern_of EDAM:0000175 ! Molecular modelling
+relationship: is_concern_of EDAM:0000175 ! Homology modelling
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000883 ! Tertiary structure
 
@@ -6976,7 +7313,7 @@ namespace: operation
 def: "Model loop conformation in protein structures." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000477 ! Protein structure comparative modelling
 relationship: is_concern_of EDAM:0000179 ! Protein tertiary structure prediction
-relationship: is_concern_of EDAM:0000175 ! Molecular modelling
+relationship: is_concern_of EDAM:0000175 ! Homology modelling
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000883 ! Tertiary structure
 
@@ -7141,7 +7478,6 @@ def: "Map the genetic architecture of dynamic complex traits." [EDAM:EBI "EMBRAC
 comment: This can involve characterization of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs
 is_a: EDAM:0000282 ! Genetic mapping
 relationship: is_concern_of EDAM:0000103 ! Genetic mapping
-relationship: is_concern_of EDAM:0000085 ! Functional genomics
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0001278 ! Genetic map
 
@@ -7378,7 +7714,6 @@ namespace: operation
 def: "Align molecular secondary structure." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000294 ! Structure-based sequence alignment
 relationship: is_concern_of EDAM:0000189 ! Structure-based sequence alignment
-relationship: is_concern_of EDAM:0000168 ! Secondary structure comparison
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000863 ! Sequence alignment
 
@@ -7403,7 +7738,7 @@ name: RNA secondary structure alignment
 namespace: operation
 def: "Align RNA secondary structures." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000500 ! Secondary structure alignment
-relationship: is_concern_of EDAM:0000099 ! RNA analysis
+relationship: is_concern_of EDAM:0000099 ! RNA
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000881 ! RNA secondary structure alignment
 
@@ -7417,7 +7752,7 @@ name: Pairwise tertiary structure alignment
 namespace: operation
 def: "Align (superimpose) exactly two molecular tertiary structures." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000295 ! Tertiary structure alignment
-relationship: is_concern_of EDAM:0000183 ! Structure alignment
+relationship: is_concern_of EDAM:0002273 ! Pairwise structure alignment
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0001479 ! Pairwise tertiary structure alignment
 
@@ -7428,7 +7763,7 @@ namespace: operation
 def: "Align (superimpose) two or more molecular tertiary structures." [EDAM:EBI "EMBRACE definition"]
 comment: This includes methods that use an existing alignment.
 is_a: EDAM:0000295 ! Tertiary structure alignment
-relationship: is_concern_of EDAM:0000183 ! Structure alignment
+relationship: is_concern_of EDAM:0002272 ! Multiple structure alignment
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0001480 ! Multiple tertiary structure alignment
 
@@ -7449,7 +7784,7 @@ name: RNA tertiary structure alignment
 namespace: operation
 def: "Align RNA tertiary structures." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000295 ! Tertiary structure alignment
-relationship: is_concern_of EDAM:0000099 ! RNA analysis
+relationship: is_concern_of EDAM:0000099 ! RNA
 relationship: is_concern_of EDAM:0000183 ! Structure alignment
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0001493 ! RNA tertiary structure alignment
@@ -7465,7 +7800,7 @@ namespace: operation
 def: "Locally align (superimpose) exactly two molecular tertiary structures." [EDAM:EBI "EMBRACE definition"]
 comment: Local alignment methods identify regions of local similarity, common substructures etc.
 is_a: EDAM:0000503 ! Pairwise tertiary structure alignment
-relationship: is_concern_of EDAM:0000183 ! Structure alignment
+relationship: is_concern_of EDAM:0002273 ! Pairwise structure alignment
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0001479 ! Pairwise tertiary structure alignment
 
@@ -7476,7 +7811,7 @@ namespace: operation
 def: "Globally align (superimpose) exactly two molecular tertiary structures." [EDAM:EBI "EMBRACE definition"]
 comment: Global alignment methods identify similarity across the entire structures.
 is_a: EDAM:0000503 ! Pairwise tertiary structure alignment
-relationship: is_concern_of EDAM:0000183 ! Structure alignment
+relationship: is_concern_of EDAM:0002273 ! Pairwise structure alignment
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0001479 ! Pairwise tertiary structure alignment
 
@@ -7494,6 +7829,7 @@ namespace: operation
 def: "Locally align (superimpose) two or more molecular tertiary structures." [EDAM:EBI "EMBRACE definition"]
 comment: Local alignment methods identify regions of local similarity, common substructures etc.
 is_a: EDAM:0000504 ! Multiple tertiary structure alignment
+relationship: is_concern_of EDAM:0002272 ! Multiple structure alignment
 relationship: is_concern_of EDAM:0000183 ! Structure alignment
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0001480 ! Multiple tertiary structure alignment
@@ -7505,6 +7841,7 @@ namespace: operation
 def: "Globally align (superimpose) two or more molecular tertiary structures." [EDAM:EBI "EMBRACE definition"]
 comment: Global alignment methods identify similarity across the entire structures.
 is_a: EDAM:0000504 ! Multiple tertiary structure alignment
+relationship: is_concern_of EDAM:0002272 ! Multiple structure alignment
 relationship: is_concern_of EDAM:0000183 ! Structure alignment
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0001480 ! Multiple tertiary structure alignment
@@ -7550,7 +7887,7 @@ namespace: operation
 def: "Align exactly two molecular profiles." [EDAM:EBI "EMBRACE definition"]
 comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons.
 is_a: EDAM:0000298 ! Profile alignment
-relationship: is_concern_of EDAM:0000188 ! Sequence profiles
+relationship: is_concern_of EDAM:0000188 ! Sequence profiles and HMMs
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000868 ! Profile alignment
 
@@ -7561,7 +7898,7 @@ name: Multiple profile alignment
 namespace: operation
 def: "Align two or more molecular profiles." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000298 ! Profile alignment
-relationship: is_concern_of EDAM:0000188 ! Sequence profiles
+relationship: is_concern_of EDAM:0000188 ! Sequence profiles and HMMs
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000868 ! Profile alignment
 
@@ -7576,7 +7913,7 @@ namespace: operation
 def: "Align exactly two molecular 3D profiles." [EDAM:EBI "EMBRACE definition"]
 comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons.
 is_a: EDAM:0000299 ! 3D profile alignment
-relationship: is_concern_of EDAM:0000183 ! Structure alignment
+relationship: is_concern_of EDAM:0002273 ! Pairwise structure alignment
 relationship: is_concern_of EDAM:0000167 ! Structural profiles
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000890 ! 3D profile alignment
@@ -7588,7 +7925,7 @@ name: Multiple 3D profile alignment
 namespace: operation
 def: "Align two or more molecular 3D profiles." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000299 ! 3D profile alignment
-relationship: is_concern_of EDAM:0000183 ! Structure alignment
+relationship: is_concern_of EDAM:0002272 ! Multiple structure alignment
 relationship: is_concern_of EDAM:0000167 ! Structural profiles
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000890 ! 3D profile alignment
@@ -7613,7 +7950,7 @@ namespace: operation
 def: "Align molecular sequence(s) to structural (3D) profile(s) or template(s) (representing a structure or structure alignment)." [EDAM:EBI "EMBRACE definition"]
 comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons.
 is_a: EDAM:0000303 ! Protein fold recognition
-relationship: is_concern_of EDAM:0000182 ! Sequence alignment
+relationship: is_concern_of EDAM:0000184 ! Sequence-structure alignment
 relationship: is_concern_of EDAM:0000167 ! Structural profiles
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000891 ! Sequence-3D profile alignment
@@ -7683,7 +8020,7 @@ namespace: operation
 def: "Design primers for large scale sequencing." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000308 ! PCR primer design
 relationship: is_concern_of EDAM:0000195 ! Polymerase chain reaction
-relationship: is_concern_of EDAM:0000102 ! Sequencing
+relationship: is_concern_of EDAM:0000102 ! Sequencing and mapping
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000841 ! Undefined
 
@@ -7823,7 +8160,7 @@ namespace: operation
 def: "Process or analyse serial analysis of gene expression (SAGE) data." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000312 ! Sequencing-based expression profile data analysis
 relationship: is_concern_of EDAM:0000203 ! Expression profiling
-relationship: is_concern_of EDAM:0000102 ! Sequencing
+relationship: is_concern_of EDAM:0000102 ! Sequencing and mapping
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000841 ! Undefined
 
@@ -7845,7 +8182,7 @@ namespace: operation
 def: "Process or analyse sequencing by synthesis (SBS) data." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000312 ! Sequencing-based expression profile data analysis
 relationship: is_concern_of EDAM:0000203 ! Expression profiling
-relationship: is_concern_of EDAM:0000102 ! Sequencing
+relationship: is_concern_of EDAM:0000102 ! Sequencing and mapping
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000841 ! Undefined
 
@@ -8280,7 +8617,7 @@ comment: Methods typically test for topological similarity between trees using f
 is_a: EDAM:0000325 ! Phylogenetic tree comparison
 relationship: is_concern_of EDAM:0000084 ! Phylogenetics
 relationship: has_input EDAM:0000841 ! Undefined
-relationship: has_output EDAM:0002245 ! Phylogenetic consensus tree
+relationship: has_output EDAM:0002247 ! Phylogenetic consensus tree
 
 
 [Term]
@@ -8366,7 +8703,7 @@ name: Peptide immunogen design
 namespace: operation
 def: "Design peptide ligands that elicit an immunological response." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000332 ! Immunogen design
-relationship: is_concern_of EDAM:0000201 ! Immunological analysis
+relationship: is_concern_of EDAM:0000201 ! Immunology
 relationship: is_concern_of EDAM:0000150 ! Protein rational design
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000841 ! Undefined
@@ -8377,7 +8714,7 @@ name: DNA vaccine design
 namespace: operation
 def: "Design DNA to elicit an immunological response." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000332 ! Immunogen design
-relationship: is_concern_of EDAM:0000201 ! Immunological analysis
+relationship: is_concern_of EDAM:0000201 ! Immunology
 relationship: is_concern_of EDAM:0000150 ! Protein rational design
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000841 ! Undefined
@@ -8489,7 +8826,7 @@ namespace: operation
 def: "Visualise RNA secondary structure, knots, pseudoknots etc." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000337 ! Visualisation and rendering
 relationship: is_concern_of EDAM:0000081 ! Structure analysis
-relationship: is_concern_of EDAM:0000099 ! RNA analysis
+relationship: is_concern_of EDAM:0000099 ! RNA
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000841 ! Undefined
 
@@ -8500,7 +8837,7 @@ namespace: operation
 def: "Visualise protein secondary structure, for example helical wheel, topology diagram etc." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000337 ! Visualisation and rendering
 relationship: is_concern_of EDAM:0000081 ! Structure analysis
-relationship: is_concern_of EDAM:0000078 ! Protein analysis
+relationship: is_concern_of EDAM:0000078 ! Proteins
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000841 ! Undefined
 
@@ -8511,7 +8848,7 @@ namespace: operation
 def: "Visualise protein transmembrane regions." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000337 ! Visualisation and rendering
 relationship: is_concern_of EDAM:0000081 ! Structure analysis
-relationship: is_concern_of EDAM:0000078 ! Protein analysis
+relationship: is_concern_of EDAM:0000078 ! Proteins
 relationship: has_input EDAM:0000841 ! Undefined
 relationship: has_output EDAM:0000841 ! Undefined
 
@@ -8985,7 +9322,7 @@ name: Informatics data resource
 namespace: resource
 def: "A database concerning biological data management and modelling, including datatypes, workflows and models." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000005 ! Data resource
-relationship: is_concern_of EDAM:0000076 ! Undefined
+relationship: is_concern_of EDAM:0002282 ! Datatypes, workflows and data handling
 relationship: is_source_of EDAM:0000843 ! Database entry
 relationship: has_identifier EDAM:0001056 ! Database name
 
@@ -9318,7 +9655,7 @@ name: Repeat sequence data resource
 namespace: resource
 def: "A database of repeat sequences." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000584 ! Sequence data resource
-relationship: is_concern_of EDAM:0000076 ! Undefined
+relationship: is_concern_of EDAM:0002262 ! Repeat sequences
 relationship: is_source_of EDAM:0000849 ! Sequence record
 relationship: is_source_of EDAM:0002044 ! Sequence data
 relationship: has_identifier EDAM:0001057 ! Sequence database name
@@ -9330,7 +9667,7 @@ name: Low complexity sequence data resource
 namespace: resource
 def: "A database of low complexity sequences." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000584 ! Sequence data resource
-relationship: is_concern_of EDAM:0000076 ! Undefined
+relationship: is_concern_of EDAM:0002263 ! Sequence complexity
 relationship: is_source_of EDAM:0000849 ! Sequence record
 relationship: is_source_of EDAM:0002044 ! Sequence data
 relationship: has_identifier EDAM:0001057 ! Sequence database name
@@ -9834,7 +10171,7 @@ comment: Small molecules include organic molecules, metal-organic compounds, sma
 is_a: EDAM:0000585 ! Structure data resource
 relationship: is_concern_of EDAM:0000076 ! Undefined
 relationship: is_source_of EDAM:0001463 ! Chemical or small molecule structure
-relationship: is_source_of EDAM:0000962 ! Chemical compound
+relationship: is_source_of EDAM:0000962 ! Chemical compound annotation
 relationship: has_identifier EDAM:0001056 ! Database name
 
 
@@ -10428,7 +10765,7 @@ name: Workflow data resource
 namespace: resource
 def: "A biological or biomedical workflow database." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000605 ! Informatics data resource
-relationship: is_concern_of EDAM:0000076 ! Undefined
+relationship: is_concern_of EDAM:0002282 ! Datatypes, workflows and data handling
 relationship: is_source_of EDAM:0000949 ! Workflow
 relationship: has_identifier EDAM:0001056 ! Database name
 
@@ -10438,7 +10775,7 @@ name: Data type, object or resource data resource
 namespace: resource
 def: "A database of data resources such as data types or objects." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000605 ! Informatics data resource
-relationship: is_concern_of EDAM:0000076 ! Undefined
+relationship: is_concern_of EDAM:0002282 ! Datatypes, workflows and data handling
 relationship: is_source_of EDAM:0000006 ! Data
 relationship: has_identifier EDAM:0001056 ! Database name
 
@@ -10448,7 +10785,7 @@ name: Biological models data resource
 namespace: resource
 def: "A database of mathematical or other biological models." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000605 ! Informatics data resource
-relationship: is_concern_of EDAM:0000076 ! Undefined
+relationship: is_concern_of EDAM:0002282 ! Datatypes, workflows and data handling
 relationship: is_source_of EDAM:0000950 ! Biological model
 relationship: has_identifier EDAM:0001056 ! Database name
 
@@ -11089,7 +11426,7 @@ consider: EDAM:0000582 ! Ontology
 id: EDAM:0000832
 name: HGNC vocabulary
 namespace: ontology
-def: "Controlled vocabulary for gene symbols and names from HUGO Gene Nomenclature Committee." [EDAM:EBI "EMBRACE definition"]
+def: "Controlled vocabulary for gene names (symbols) from HUGO Gene Nomenclature Committee." [EDAM:EBI "EMBRACE definition"]
 is_obsolete: true
 consider: EDAM:0000582 ! Ontology
 ! is_a: EDAM:0000582 ! Ontology
@@ -11208,7 +11545,7 @@ id: EDAM:0000842
 name: Identifier
 namespace: data
 def: "Something that identifies (typically uniquely) an entity, databasem, ontology or datatype." [EDAM:EBI "EMBRACE definition"]
-comment: This term is used for datatypes with the sole purpose of identification.  It is not used for datatypes which contain other fields not related to identification.
+comment: This term is used for datatypes with the sole purpose of identification. It is not used for datatypes which contain other fields not related to identification.
 is_a: EDAM:0000006 ! Data
 relationship: is_identifier_of EDAM:0000002 ! Biological entity
 relationship: is_identifier_of EDAM:0000005 ! Data resource
@@ -11219,6 +11556,19 @@ relationship: is_output_of EDAM:0000004 ! Operation
 relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
+id: EDAM:0002248
+name: Schema
+namespace: data
+def: "A data schema for organising or transforming data of some type." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0000006 ! Data
+relationship: is_attribute_of EDAM:0000008 ! Undefined
+relationship: is_input_of EDAM:0000223 ! Undefined
+relationship: is_output_of EDAM:0000223 ! Undefined
+relationship: has_source EDAM:0000580 ! Undefined
+relationship: has_identifier EDAM:0000841 ! Undefined
+
+
+[Term]
 id: EDAM:0000581
 name: Database
 namespace: resource
@@ -11333,7 +11683,7 @@ relationship: has_identifier EDAM:0000841 ! Undefined
 id: EDAM:0002044
 name: Sequence data
 namespace: data
-def: "Sequence-associated data, typically one or more molecular sequences (or sequence identifiers) and associated annotation.   The sequences might be aligned or unaligned.  The annotation might include positional features (such as a feature table) or non-positional properties." [EDAM:EBI "EMBRACE definition"]
+def: "Sequence-associated data, typically one or more molecular sequences (or sequence identifiers) and associated annotation. The sequences might be aligned or unaligned. The annotation might include positional features (such as a feature table) or non-positional properties." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000006 ! Data
 relationship: is_attribute_of EDAM:0000008 ! Undefined
 relationship: is_input_of EDAM:0000223 ! Undefined
@@ -11483,7 +11833,7 @@ relationship: has_identifier EDAM:0000841 ! Undefined
 id: EDAM:0000867
 name: Sequence alignment annotation
 namespace: data
-def: "An informative report of molecular sequence alignment-derived data or metadata.  This will typically include at least basic information such as a description, sequence identifiers, alignment score etc." [EDAM:EBI "EMBRACE definition"]
+def: "An informative report of molecular sequence alignment-derived data or metadata. This will typically include at least basic information such as a description, sequence identifiers, alignment score etc." [EDAM:EBI "EMBRACE definition"]
 comment: This is a broad data type and is used a placeholder for other, more specific types.
 is_a: EDAM:0002083 ! Alignment annotation
 relationship: is_attribute_of EDAM:0000008 ! Undefined
@@ -11734,7 +12084,7 @@ id: EDAM:0000895
 name: Peptide
 namespace: data
 def: "An informative report about a specific peptide." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000962 ! Chemical compound
+is_a: EDAM:0000962 ! Chemical compound annotation
 relationship: is_attribute_of EDAM:0000008 ! Undefined
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
@@ -11788,6 +12138,20 @@ relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 relationship: has_identifier EDAM:0000841 ! Undefined
 
+
+[Term]
+id: EDAM:0002313
+name: Carbohydrate structure annotation
+namespace: data
+def: "Annotation on or information derived from a specific carbohydrate 3D structure." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0002085 ! Structure annotation
+relationship: is_attribute_of EDAM:0000008 ! Undefined
+relationship: is_input_of EDAM:0000223 ! Undefined
+relationship: is_output_of EDAM:0000223 ! Undefined
+relationship: has_source EDAM:0000580 ! Undefined
+relationship: has_identifier EDAM:0000841 ! Undefined
+
+
 [Term]
 id: EDAM:0000898
 name: Protein structure-derived report
@@ -11879,7 +12243,7 @@ id: EDAM:0000911
 name: Nucleotide base
 namespace: data
 def: "An informative report about a specific nucleotide base." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000962 ! Chemical compound
+is_a: EDAM:0000962 ! Chemical compound annotation
 relationship: is_attribute_of EDAM:0000008 ! Undefined
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
@@ -11975,6 +12339,7 @@ name: Gene annotation
 namespace: data
 def: "An informative report on a particular locus, gene, gene system or groups of genes." [EDAM:EBI "EMBRACE definition"]
 comment: This might include the gene name, description, summary and so on.
+synonym: "Gene report" EXACT []
 xref: Moby:gene
 xref: Moby:GeneInfo
 xref: Moby_namespace:Human_Readable_Description
@@ -12261,7 +12626,7 @@ relationship: has_identifier EDAM:0000841 ! Undefined
 
 [Term]
 id: EDAM:0000962
-name: Chemical compound
+name: Chemical compound annotation
 namespace: data
 def: "An informative report on a specific chemical compound." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000006 ! Data
@@ -12277,9 +12642,10 @@ relationship: has_identifier EDAM:0001086 ! Chemical compound identifier
 
 [Term]
 id: EDAM:0000963
-name: Organism strain data
+name: Cell line
 namespace: data
-def: "Report on a particular strain of organism cell line including plants, virus, fungi and bacteria.  The data typically includes strain number, organism type, growth conditions, source and so on." [EDAM:EBI "EMBRACE definition"]
+def: "Report on a particular strain of organism cell line including plants, virus, fungi and bacteria. The data typically includes strain number, organism type, growth conditions, source and so on." [EDAM:EBI "EMBRACE definition"]
+synonym: "Organism strain data" EXACT []
 is_a: EDAM:0000006 ! Data
 relationship: is_attribute_of EDAM:0000008 ! Undefined
 relationship: is_input_of EDAM:0000223 ! Undefined
@@ -12287,6 +12653,17 @@ relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 relationship: has_identifier EDAM:0000841 ! Undefined
 
+[Term]
+id: EDAM:0002307
+name: Virus report
+namespace: data
+def: "An informative report on a specific virus." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0000006 ! Data
+relationship: is_attribute_of EDAM:0000008 ! Undefined
+relationship: is_input_of EDAM:0000223 ! Undefined
+relationship: is_output_of EDAM:0000223 ! Undefined
+relationship: has_source EDAM:0000580 ! Undefined
+relationship: has_identifier EDAM:0000841 ! Undefined
 
 
 
@@ -12603,10 +12980,11 @@ relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
 id: EDAM:0001893
-name: Locus identifier
+name: Locus ID
 namespace: data
-def: "A unique name or other identifier of a genetic locus." [EDAM:EBI "EMBRACE definition"]
+def: "A unique name or other identifier of a genetic locus, typically conforming to a scheme that names loci (such as predicted genes) depending on their position in a molecular sequence, for example a completely sequenced genome or chromosome." [EDAM:EBI "EMBRACE definition"]
 synonym: "Locus name" EXACT []
+synonym: "Locus identifier" EXACT []
 is_a: EDAM:0000842 ! Identifier
 relationship: is_identifier_of EDAM:0001894 ! Locus
 relationship: is_input_of EDAM:0000223 ! Undefined
@@ -12617,8 +12995,7 @@ relationship: has_source EDAM:0000580 ! Undefined
 id: EDAM:0001025
 name: Gene identifier
 namespace: data
-def: "A unique identifier of a gene." [EDAM:EBI "EMBRACE definition"]
-synonym: "Gene code" EXACT []
+def: "An identifier of a gene, such as a name/symbol or a unique identifier of a gene in a database." [EDAM:EBI "EMBRACE definition"]
 xref: Moby:GeneAccessionList
 is_a: EDAM:0000842 ! Identifier
 relationship: is_identifier_of EDAM:0000051 ! Gene
@@ -12655,7 +13032,6 @@ id: EDAM:0001867
 name: Protein fold name
 namespace: data
 def: "The name of a protein fold." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000842 ! Identifier
 is_a: EDAM:0002099 ! Name
 relationship: is_identifier_of EDAM:0000065 ! Protein domain
 relationship: is_input_of EDAM:0000223 ! Undefined
@@ -12789,6 +13165,34 @@ relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
+id: EDAM:0002294
+name: Sequence variation identifier
+namespace: data
+def: "An identifier of an entry from a database of molecular sequence variation." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0000842 ! Identifier
+relationship: is_identifier_of EDAM:0000008 ! Undefined
+relationship: is_input_of EDAM:0000223 ! Undefined
+relationship: is_output_of EDAM:0000223 ! Undefined
+relationship: has_source EDAM:0000580 ! Undefined
+
+
+[Term]
+id: EDAM:0001094
+name: Sequence type name
+namespace: data
+def: "The name of a type of a molecular sequence." [EDAM:EBI "EMBRACE definition"]
+comment: Sequence type might reflect the molecule (protein, nucleic acid etc) or the sequence itself (gapped, ambiguous etc).
+is_a: EDAM:0000842 ! Identifier
+is_a: EDAM:0002100 ! Type
+relationship: is_identifier_of EDAM:0002044 ! Sequence data
+relationship: is_identifier_of EDAM:0000849 ! Sequence record
+relationship: is_input_of EDAM:0000223 ! Undefined
+relationship: is_output_of EDAM:0000223 ! Undefined
+relationship: has_source EDAM:0000580 ! Undefined
+
+
+
+[Term]
 id: EDAM:0001064
 name: Sequence set identifier
 namespace: data
@@ -13046,7 +13450,6 @@ id: EDAM:0002219
 name: Database field name
 namespace: data
 def: "The name of a field in a database." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000842 ! Identifier
 is_a: EDAM:0002099 ! Name
 relationship: is_identifier_of EDAM:0000008 ! Undefined
 relationship: is_input_of EDAM:0000223 ! Undefined
@@ -13073,7 +13476,7 @@ def: "Identifier of an entry from a database of chemicals." [EDAM:EBI "EMBRACE d
 synonym: "Small molecule identifier" EXACT []
 is_a: EDAM:0000842 ! Identifier
 is_a: EDAM:0000982 ! Molecule identifier
-relationship: is_identifier_of EDAM:0000962 ! Chemical compound
+relationship: is_identifier_of EDAM:0000962 ! Chemical compound annotation
 relationship: is_identifier_of EDAM:0000015 ! Small molecule
 relationship: is_identifier_of EDAM:0001712 ! Chemical structure image
 relationship: is_identifier_of EDAM:0000846 ! Chemical formula
@@ -13149,7 +13552,6 @@ id: EDAM:0002129
 name: File format name
 namespace: data
 def: "Name of a file format such as HTML, PNG, PDF, EMBL, GenBank and so on." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000842 ! Identifier
 is_a: EDAM:0002099 ! Name
 relationship: is_identifier_of EDAM:0000008 ! Undefined
 relationship: is_input_of EDAM:0000223 ! Undefined
@@ -13161,7 +13563,6 @@ id: EDAM:0002131
 name: Operating system name
 namespace: data
 def: "Name of a computer operating system such as Linux, PC or Mac." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000842 ! Identifier
 is_a: EDAM:0002099 ! Name
 relationship: is_identifier_of EDAM:0000008 ! Undefined
 relationship: is_input_of EDAM:0000223 ! Undefined
@@ -13196,7 +13597,6 @@ id: EDAM:0002133
 name: Logical operator
 namespace: data
 def: "A logical operator such as OR, AND, XOR, and NOT." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000842 ! Identifier
 is_a: EDAM:0002099 ! Name
 relationship: is_identifier_of EDAM:0000008 ! Undefined
 relationship: is_input_of EDAM:0000223 ! Undefined
@@ -13398,7 +13798,7 @@ relationship: has_source EDAM:0000580 ! Undefined
 id: EDAM:0000995
 name: Nucleotide identifier
 namespace: data
-def: "Name or other identifier of an amino acid." [EDAM:EBI "EMBRACE definition"]
+def: "Name or other identifier of a nucleotide." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0001086 ! Chemical compound identifier
 relationship: is_identifier_of EDAM:0000022 ! Nucleotide
 relationship: is_input_of EDAM:0000223 ! Undefined
@@ -13424,7 +13824,7 @@ def: "Chemical structure specified in PubChem Compound Identification (CID), a n
 synonym: "PubChem compound accession identifier" EXACT []
 is_a: EDAM:0001086 ! Chemical compound identifier
 is_a: EDAM:0002091 ! Accession
-relationship: is_identifier_of EDAM:0000962 ! Chemical compound
+relationship: is_identifier_of EDAM:0000962 ! Chemical compound annotation
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
@@ -13436,19 +13836,20 @@ namespace: data
 def: "Identifier of an entry from the ChemSpider database." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0001086 ! Chemical compound identifier
 is_a: EDAM:0002091 ! Accession
-relationship: is_identifier_of EDAM:0000962 ! Chemical compound
+relationship: is_identifier_of EDAM:0000962 ! Chemical compound annotation
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
 id: EDAM:0001174
-name: ChEBI identifier
+name: ChEBI ID
 namespace: data
 def: "Identifier of an entry from the ChEBI database." [EDAM:EBI "EMBRACE definition"]
+synonym: "ChEBI identifier" EXACT []
 is_a: EDAM:0001086 ! Chemical compound identifier
 is_a: EDAM:0002091 ! Accession
-relationship: is_identifier_of EDAM:0000962 ! Chemical compound
+relationship: is_identifier_of EDAM:0000962 ! Chemical compound annotation
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
@@ -13459,7 +13860,7 @@ name: BioCyc compound ID
 namespace: data
 def: "Identifier of a compound from the BioCyc chemical compounds database." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002104 ! BioCyc identifier
-relationship: is_identifier_of EDAM:0000962 ! Chemical compound
+relationship: is_identifier_of EDAM:0000962 ! Chemical compound annotation
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
@@ -13600,6 +14001,20 @@ relationship: has_source EDAM:0000580 ! Undefined
 !
 ! Data<-Identifier<-Molecule identifier<-Chemical compound identifier<-Drug identifier
 !
+[Term]
+id: EDAM:0002326
+name: DrugBank ID
+namespace: data
+def: "Unique identifier of a drug from the DrugBank database." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0000993 ! Drug identifier
+is_a: EDAM:0002091 ! Accession
+relationship: is_identifier_of EDAM:0000020 ! Drug
+relationship: is_input_of EDAM:0000223 ! Undefined
+relationship: is_output_of EDAM:0000223 ! Undefined
+relationship: has_source EDAM:0000580 ! Undefined
+
+
+
 
 !
 ! Data<-Identifier<-Molecule identifier<-Chemical compound identifier<-Amino acid identifier
@@ -13687,10 +14102,11 @@ relationship: has_source EDAM:0000580 ! Undefined
 !
 [Term]
 id: EDAM:0001008
-name: Polypeptide chain identifier
+name: Polypeptide chain ID
 namespace: data
 def: "Identifier of a polypeptide chain from a protein." [EDAM:EBI "EMBRACE definition"]
-comment: This is typically a character (for the chain) appended to a PDB identifier.
+comment: This is typically a character (for the chain) appended to a PDB identifier, e.g. 1cukA
+synonym: "Polypeptide chain identifier" EXACT []
 synonym: "Protein chain identifier" EXACT []
 synonym: "PDB chain identifier" EXACT []
 synonym: "Chain identifier" EXACT []
@@ -13771,21 +14187,19 @@ relationship: has_source EDAM:0000580 ! Undefined
 ! Data<-Identifier<-Molecule identifier<-Protein identifier<-Enzyme identifier
 !
 [Term]
-id: EDAM:0001011
-name: Enzyme Commission number
+id: EDAM:0002321
+name: Enzyme accession
 namespace: data
-def: "An Enzyme Commission (EC) number of an enzyme." [EDAM:EBI "EMBRACE definition"]
-synonym: "EC number" EXACT []
-xref: Moby:EC_Number
-xref: Moby:Annotated_EC_Number
+def: "A unique, persistent identifier of an enzyme." [EDAM:EBI "EMBRACE definition"]
+synonym: "Enzyme ID" EXACT []
 is_a: EDAM:0001010 ! Enzyme identifier
 is_a: EDAM:0002091 ! Accession
 relationship: is_identifier_of EDAM:0000039 ! Enzyme
-relationship: is_identifier_of EDAM:0001509 ! Enzyme annotation
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
+
 [Term]
 id: EDAM:0001012
 name: Enzyme name
@@ -13798,20 +14212,52 @@ relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
+!
+! Data<-Identifier<-Molecule identifier<-Protein identifier<-Enzyme identifier<-Enzyme accession
+!
+[Term]
+id: EDAM:0001011
+name: EC number
+namespace: data
+def: "An Enzyme Commission (EC) number of an enzyme." [EDAM:EBI "EMBRACE definition"]
+synonym: "Enzyme Commission number" EXACT []
+xref: Moby:EC_Number
+xref: Moby:Annotated_EC_Number
+is_a: EDAM:0002091 ! Enzyme accession
+relationship: is_identifier_of EDAM:0000039 ! Enzyme
+relationship: is_identifier_of EDAM:0001509 ! Enzyme annotation
+relationship: is_input_of EDAM:0000223 ! Undefined
+relationship: is_output_of EDAM:0000223 ! Undefined
+relationship: has_source EDAM:0000580 ! Undefined
+
 [Term]
 id: EDAM:0002107
-name: BioCyc enzyme ID
+name: Enzyme ID (BioCyc)
 namespace: data
 def: "Identifier of an enzyme from the BioCyc enzymes database." [EDAM:EBI "EMBRACE definition"]
+synonym: "BioCyc enzyme ID" EXACT []
 is_a: EDAM:0002104 ! BioCyc identifier
-is_a: EDAM:0001010 ! Enzyme identifier
+is_a: EDAM:0002091 ! Enzyme accession
+relationship: is_identifier_of EDAM:0000008 ! Undefined
+relationship: is_input_of EDAM:0000223 ! Undefined
+relationship: is_output_of EDAM:0000223 ! Undefined
+relationship: has_source EDAM:0000580 ! Undefined
+
+
+[Term]
+id: EDAM:0002325
+name: REBASE enzyme number
+namespace: data
+def: "Identifier of an enzyme from the REBASE enzymes database." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0002091 ! Enzyme accession
 relationship: is_identifier_of EDAM:0000008 ! Undefined
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
+
 !
-! Data<-Identifier<-Molecule identifier<-Protein identifier<-Enzyme identifier<-Enzyme Commission number
+! Data<-Identifier<-Molecule identifier<-Protein identifier<-Enzyme identifier<-EC number
 !
 
 
@@ -13926,7 +14372,7 @@ consider: EDAM:0002116 ! Codon
 
 
 !
-! Data<-Identifier<-Locus identifier
+! Data<-Identifier<-Locus ID
 !
 
 ! Don't know whether the loci identifiers listered here are 'ordered' or not.
@@ -13935,20 +14381,17 @@ id: EDAM:0002009
 name: Ordered locus name
 namespace: data
 def: "A name for a genetic locus conforming to a scheme that names loci (such as predicted genes) depending on their position in a molecular sequence, for example a completely sequenced genome or chromosome." [EDAM:EBI "EMBRACE definition"]
-synonym: "Ordered locus identifier" EXACT []
-is_a: EDAM:0001893 ! Locus identifier
-relationship: is_identifier_of EDAM:0001894 ! Locus
-relationship: is_input_of EDAM:0000223 ! Undefined
-relationship: is_output_of EDAM:0000223 ! Undefined
-relationship: has_source EDAM:0000580 ! Undefined
+is_obsolete: true
+consider: EDAM:0001893 ! Locus ID
 
 [Term]
 id: EDAM:0001895
-name: AGI locus code
+name: Locus ID (AGI)
 namespace: data
 def: "Locus identifier for Arabidopsis Genome Initiative (TAIR, TIGR and MIPS databases)" [EDAM:EBI "EMBRACE definition"]
+synonym: "AGI locus code" EXACT []
 xref: http://www.geneontology.org/doc/GO.xrf_abbs:AGI_LocusCode
-is_a: EDAM:0001893 ! Locus identifier
+is_a: EDAM:0001893 ! Locus ID
 relationship: is_identifier_of EDAM:0001894 ! Locus
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
@@ -13957,12 +14400,12 @@ relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
 id: EDAM:0001896
-name: ASPGD locus identifier
+name: Locus ID (ASPGD)
 namespace: data
 def: "Identifier for loci from ASPGD (Aspergillus Genome Database)." [EDAM:EBI "EMBRACE definition"]
 xref: http://www.geneontology.org/doc/GO.xrf_abbs: ASPGD
 xref: http://www.geneontology.org/doc/GO.xrf_abbs: ASPGDID
-is_a: EDAM:0001893 ! Locus identifier
+is_a: EDAM:0001893 ! Locus ID
 relationship: is_identifier_of EDAM:0001894 ! Locus
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
@@ -13971,11 +14414,11 @@ relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
 id: EDAM:0001897
-name: MGG locus identifier
+name: Locus ID (MGG)
 namespace: data
 def: "Identifier for loci from Magnaporthe grisea Database at the Broad Institute." [EDAM:EBI "EMBRACE definition"]
 xref: http://www.geneontology.org/doc/GO.xrf_abbs: Broad_MGG
-is_a: EDAM:0001893 ! Locus identifier
+is_a: EDAM:0001893 ! Locus ID
 relationship: is_identifier_of EDAM:0001894 ! Locus
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
@@ -13983,13 +14426,14 @@ relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
 id: EDAM:0001898
-name: CGDID
+name: Locus ID (CGD)
 namespace: data
 def: "Identifier for loci from CGD (Candida Genome Database)." [EDAM:EBI "EMBRACE definition"]
 synonym: "CGD locus identifier" EXACT []
+synonym: "CGDID" EXACT []
 xref: http://www.geneontology.org/doc/GO.xrf_abbs: CGD
 xref: http://www.geneontology.org/doc/GO.xrf_abbs: CGDID
-is_a: EDAM:0001893 ! Locus identifier
+is_a: EDAM:0001893 ! Locus ID
 relationship: is_identifier_of EDAM:0001894 ! Locus
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
@@ -13997,12 +14441,12 @@ relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
 id: EDAM:0001899
-name: CMR locus identifier
+name: Locus ID (CMR)
 namespace: data
 def: "Locus identifier for Comprehensive Microbial Resource at the J. Craig Venter Institute." [EDAM:EBI "EMBRACE definition"]
 xref: http://www.geneontology.org/doc/GO.xrf_abbs: JCVI_CMR
 xref: http://www.geneontology.org/doc/GO.xrf_abbs: TIGR_CMR
-is_a: EDAM:0001893 ! Locus identifier
+is_a: EDAM:0001893 ! Locus ID
 relationship: is_identifier_of EDAM:0001894 ! Locus
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
@@ -14013,9 +14457,10 @@ id: EDAM:0001900
 name: NCBI locus tag
 namespace: data
 def: "Identifier for loci from NCBI database." [EDAM:EBI "EMBRACE definition"]
+synonym: "Locus ID (NCBI)" EXACT []
 xref: http://www.geneontology.org/doc/GO.xrf_abbs: NCBI_locus_tag
 xref: Moby_namespace:LocusID
-is_a: EDAM:0001893 ! Locus identifier
+is_a: EDAM:0001893 ! Locus ID
 relationship: is_identifier_of EDAM:0001894 ! Locus
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
@@ -14023,12 +14468,12 @@ relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
 id: EDAM:0001901
-name: SGD locus identifier
+name: Locus ID (SGD)
 namespace: data
 def: "Identifier for loci from SGD (Saccharomyces Genome Database)." [EDAM:EBI "EMBRACE definition"]
 xref: http://www.geneontology.org/doc/GO.xrf_abbs: SGD
 xref: http://www.geneontology.org/doc/GO.xrf_abbs: SGDID
-is_a: EDAM:0001893 ! Locus identifier
+is_a: EDAM:0001893 ! Locus ID
 relationship: is_identifier_of EDAM:0001894 ! Locus
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
@@ -14036,11 +14481,11 @@ relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
 id: EDAM:0001902
-name: MMP locus identifier
+name: Locus ID (MMP)
 namespace: data
 def: "Identifier of loci from Maize Mapping Project." [EDAM:EBI "EMBRACE definition"]
 xref: Moby_namespace:MMP_Locus
-is_a: EDAM:0001893 ! Locus identifier
+is_a: EDAM:0001893 ! Locus ID
 relationship: is_identifier_of EDAM:0001894 ! Locus
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
@@ -14048,11 +14493,11 @@ relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
 id: EDAM:0001903
-name: DictyBase locus identifier
+name: Locus ID (DictyBase)
 namespace: data
 def: "Identifier of locus from DictyBase (Dictyostelium discoideum)." [EDAM:EBI "EMBRACE definition"]
 xref: Moby_namespace:DDB_gene
-is_a: EDAM:0001893 ! Locus identifier
+is_a: EDAM:0001893 ! Locus ID
 relationship: is_identifier_of EDAM:0001894 ! Locus
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
@@ -14060,12 +14505,12 @@ relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
 id: EDAM:0001904
-name: EntrezGene locus identifier
+name: Locus ID (EntrezGene)
 namespace: data
 def: "Identifier of a locus from EntrezGene database." [EDAM:EBI "EMBRACE definition"]
 xref: Moby_namespace:EntrezGene_EntrezGeneID
 xref: Moby_namespace:EntrezGene_ID
-is_a: EDAM:0001893 ! Locus identifier
+is_a: EDAM:0001893 ! Locus ID
 relationship: is_identifier_of EDAM:0001894 ! Locus
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
@@ -14073,11 +14518,11 @@ relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
 id: EDAM:0001905
-name: MaizeGDB locus identifier
+name: Locus ID (MaizeGDB)
 namespace: data
 def: "Identifier of locus from MaizeGDB (Maize genome database)." [EDAM:EBI "EMBRACE definition"]
 xref: Moby_namespace:MaizeGDB_Locus
-is_a: EDAM:0001893 ! Locus identifier
+is_a: EDAM:0001893 ! Locus ID
 relationship: is_identifier_of EDAM:0001894 ! Locus
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
@@ -14086,11 +14531,11 @@ relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
 id: EDAM:0001908
-name: Tropgene locus identifier
+name: Locus ID (Tropgene)
 namespace: data
 def: "Identifier of a locus from the Tropgene database." [EDAM:EBI "EMBRACE definition"]
 xref: Moby:Tropgene_locus
-is_a: EDAM:0001893 ! Locus identifier
+is_a: EDAM:0001893 ! Locus ID
 relationship: is_identifier_of EDAM:0001894 ! Locus
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
@@ -14103,9 +14548,9 @@ relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
 id: EDAM:0001026
-name: Gene name
+name: Gene symbol
 namespace: data
-def: "Name of a gene." [EDAM:EBI "EMBRACE definition"]
+def: "The short name of a gene; a single word that does not contain whitespace characters. It is typically derived from the the gene name." [EDAM:EBI "EMBRACE definition"]
 synonym: "Gene symbol" EXACT []
 xref: Moby_namespace:Global_GeneSymbol
 xref: Moby_namespace:Global_GeneCommonName
@@ -14116,575 +14561,701 @@ relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
-id: EDAM:0001891
-name: iHOP symbol
+id: EDAM:0002299
+name: Gene name
 namespace: data
-def: "A unique identifier of a protein or gene used in the iHOP database." [EDAM:EBI "EMBRACE definition"]
-xref: Moby_namespace:iHOPsymbol
+def: "The name of a gene, (typically) assigned by a person and/or according to a naming scheme. It may contain whitespace characters and is typically more intuitive and readable than a gene symbol. It (typically) may be used to identify similar genes in different species and to derive a gene symbol." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0001025 ! Gene identifier
-is_a: EDAM:0001026 ! Protein identifier
 relationship: is_identifier_of EDAM:0000051 ! Gene
-relationship: is_identifier_of EDAM:0000037 ! Protein
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
 
 [Term]
-id: EDAM:0001027
-name: NCBI gene ID
+id: EDAM:0002295
+name: Gene ID
 namespace: data
-def: "An NCBI unique identifier of a gene." [EDAM:EBI "EMBRACE definition"]
-synonym: "Gene identifier (NCBI)" EXACT []
-xref: http://www.geneontology.org/doc/GO.xrf_abbs:NCBI_Gene
-xref: http://www.geneontology.org/doc/GO.xrf_abbs:LocusID
+def: "A unique (and typically persistent) identifier of a gene in a database, that is (typically) different to the gene name/symbol." [EDAM:EBI "EMBRACE definition"]
+synonym: "Gene code" EXACT []
+synonym: "Gene accession" EXACT []
 is_a: EDAM:0001025 ! Gene identifier
-! relationship: is_identifier_of EDAM:0001782 ! NCBI gene report format
+is_a: EDAM:0002091 ! Accession
+relationship: is_identifier_of EDAM:0000051 ! Gene
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
 
 [Term]
-id: EDAM:0001028
-name: Gene identifier (NCBI RefSeq)
-namespace: data
-def: "An NCBI RefSeq unique identifier of a gene." [EDAM:EBI "EMBRACE definition"]
-is_obsolete: true
-consider: EDAM:0001027 ! NCBI gene ID
-
-[Term]
-id: EDAM:0001029
-name: Gene identifier (NCBI UniGene)
-namespace: data
-def: "An NCBI UniGene unique identifier of a gene." [EDAM:EBI "EMBRACE definition"]
-is_obsolete: true
-consider: EDAM:0001104 ! UniGene cluster ID
-
-[Term]
-id: EDAM:0001030
-name: Gene identifier (Entrez)
-namespace: data
-def: "An Entrez unique identifier of a gene." [EDAM:EBI "EMBRACE definition"]
-is_obsolete: true
-consider: EDAM:0001027 ! NCBI gene ID
-
-
-[Term]
-id: EDAM:0001031
-name: CGD ID
+id: EDAM:0001891
+name: iHOP symbol
 namespace: data
-def: "Identifier of a gene or feature from the CGD database." [EDAM:EBI "EMBRACE definition"]
+def: "A unique identifier of a protein or gene used in the iHOP database." [EDAM:EBI "EMBRACE definition"]
+xref: Moby_namespace:iHOPsymbol
 is_a: EDAM:0001025 ! Gene identifier
-! relationship: is_identifier_of EDAM:0001605 ! CGD gene report format
+is_a: EDAM:0000989 ! Protein identifier
+relationship: is_identifier_of EDAM:0000051 ! Gene
+relationship: is_identifier_of EDAM:0000037 ! Protein
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
+! Suspect this identifiers more than just genes
 [Term]
-id: EDAM:0001032
-name: DictyBase ID
+id: EDAM:0001036
+name: TIGR identifier
 namespace: data
-def: "Identifier of a gene from DictyBase." [EDAM:EBI "EMBRACE definition"]
+def: "Identifier of an entry from the TIGR database." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0001025 ! Gene identifier
-is_a: EDAM:0002091 ! Accession
-! relationship: is_identifier_of EDAM:0001604 ! DictyBase gene report format
+! relationship: is_identifier_of EDAM:0001619 ! TIGR entry
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
+! Suspect this identifiers more than just genes
 [Term]
-id: EDAM:0001033
-name: Ensembl ID
+id: EDAM:0001037
+name: TAIR identifier
 namespace: data
-def: "Unique identifier for a gene from the Ensembl database." [EDAM:EBI "EMBRACE definition"]
+def: "Identifier of an entry from the TAIR database." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0001025 ! Gene identifier
-is_a: EDAM:0002091 ! Accession
-! relationship: is_identifier_of EDAM:0001603 ! Ensembl gene report format
+! relationship: is_identifier_of EDAM:0001616 ! TAIR entry
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
+
+
+
+!
+! Data<-Identifier<-Gene identifier<-Gene name
+! 
+
 [Term]
-id: EDAM:0001034
-name: SGD identifier
+id: EDAM:0001806
+name: Gene synonym
 namespace: data
-def: "Identifier of an entry from the SGD database." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0001025 ! Gene identifier
-! relationship: is_identifier_of EDAM:0001614 ! SGD gene report format
-relationship: is_input_of EDAM:0000223 ! Undefined
-relationship: is_output_of EDAM:0000223 ! Undefined
-relationship: has_source EDAM:0000580 ! Undefined
+def: "Any name (other than the recommended one) for a gene." [EDAM:EBI "EMBRACE definition"]
+synonym: "Gene name synonym" EXACT []
+is_obsolete: true
+consider: EDAM:0001026 ! Gene name
+
 
 [Term]
-id: EDAM:0001035
-name: GeneDB identifier
+id: EDAM:0001807
+name: ORF name
 namespace: data
-def: "Identifier of an entry from the GeneDB database." [EDAM:EBI "EMBRACE definition"]
-xref: Moby_namespace:GeneDB
-is_a: EDAM:0001025 ! Gene identifier
-! relationship: is_identifier_of EDAM:0001615 ! GeneDB entry
+def: "The name of an open reading frame attributed by a sequencing project." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0002299 ! Gene name
+relationship: is_identifier_of EDAM:0000051 ! Gene
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
+
+! GeneFarm gene ID is also given
 [Term]
-id: EDAM:0001036
-name: TIGR identifier
+id: EDAM:0001892
+name: Gene name (GeneFarm)
 namespace: data
-def: "Identifier of an entry from the TIGR database." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0001025 ! Gene identifier
-! relationship: is_identifier_of EDAM:0001619 ! TIGR entry
+def: "Name of a gene from the GeneFarm database." [EDAM:EBI "EMBRACE definition"]
+xref: Moby_namespace:GENEFARM_GeneName
+is_a: EDAM:0001026 ! Gene symbol
+relationship: is_identifier_of EDAM:0000051 ! Gene
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
 
 [Term]
-id: EDAM:0001037
-name: TAIR identifier
+id: EDAM:0001889
+name: Gene name (DragonDB)
 namespace: data
-def: "Identifier of an entry from the TAIR database." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0001025 ! Gene identifier
-! relationship: is_identifier_of EDAM:0001616 ! TAIR entry
+def: "The name of an Antirrhinum Gene from the DragonDB database." [EDAM:EBI "EMBRACE definition"]
+xref: Moby_namespace:DragonDB_Gene
+is_a: EDAM:0001026 ! Gene symbol
+relationship: is_identifier_of EDAM:0000051 ! Gene
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
+
 [Term]
-id: EDAM:0001885
-name: GeneFarm gene identifier
+id: EDAM:0001890
+name: Gene name (Arabidopsis)
 namespace: data
-def: "Identifier of a gene from the GeneFarm database." [EDAM:EBI "EMBRACE definition"]
-xref: Moby_namespace:GENEFARM_GeneID
-is_a: EDAM:0001025 ! Gene identifier
-relationship: is_identifier_of EDAM:0000008 ! Undefined
+def: "A unique identifier for an Arabidopsis gene, which is an acronym or abbreviation of the gene name." [EDAM:EBI "EMBRACE definition"]
+xref: Moby_namespace:ArabidopsisGeneSymbol
+is_a: EDAM:0001026 ! Gene symbol
+relationship: is_identifier_of EDAM:0000051 ! Gene
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
-
 [Term]
-id: EDAM:0001886
-name: Blattner number
+id: EDAM:0001783
+name: Gene name (ASPGD)
 namespace: data
-def: "The blattner identifier for a gene." [EDAM:EBI "EMBRACE definition"]
-xref: Moby_namespace:Blattner_number
-is_a: EDAM:0001025 ! Gene identifier
-relationship: is_identifier_of EDAM:0000008 ! Undefined
+def: "Name of a gene from Aspergillus Genome Database." [EDAM:EBI "EMBRACE definition"]
+xref: http://www.geneontology.org/doc/GO.xrf_abbs:ASPGD_LOCUS
+is_a: EDAM:0001026 ! Gene symbol
+relationship: is_identifier_of EDAM:0000051 ! Gene
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
-id: EDAM:0001887
-name: MIPS genetic element identifier (Maize)
+id: EDAM:0001784
+name: Gene name (CGD)
 namespace: data
-def: "Identifier for genetic elements in MIPS Maize database." [EDAM:EBI "EMBRACE definition"]
-xref: Moby_namespace:MIPS_GE_Maize
-is_a: EDAM:0001025 ! Gene identifier
-relationship: is_identifier_of EDAM:0000008 ! Undefined
+def: "Name of a gene from Candida Genome Database." [EDAM:EBI "EMBRACE definition"]
+xref: http://www.geneontology.org/doc/GO.xrf_abbs:CGD_LOCUS
+is_a: EDAM:0001026 ! Gene symbol
+relationship: is_identifier_of EDAM:0000051 ! Gene
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
-id: EDAM:0001888
-name:  MIPS genetic element identifier (Medicago)
+id: EDAM:0001785
+name: Gene name (dictyBase)
 namespace: data
-def: "Identifier for genetic elements in MIPS Medicago database." [EDAM:EBI "EMBRACE definition"]
-xref: Moby_namespace:MIPS_GE_Medicago
-is_a: EDAM:0001025 ! Gene identifier
-relationship: is_identifier_of EDAM:0000008 ! Undefined
+def: "Name of a gene from dictyBase database." [EDAM:EBI "EMBRACE definition"]
+xref: http://www.geneontology.org/doc/GO.xrf_abbs:dictyBase
+is_a: EDAM:0001026 ! Gene symbol
+relationship: is_identifier_of EDAM:0000051 ! Gene
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
-
 [Term]
-id: EDAM:0001907
-name: KOME gene identifier
+id: EDAM:0001786
+name: Gene name (EcoGene primary)
 namespace: data
-def: "Identifier of a gene from the KOME database." [EDAM:EBI "EMBRACE definition"]
-xref: Moby_namespace:GeneId
-is_a: EDAM:0001025 ! Gene identifier
-relationship: is_identifier_of EDAM:0000008 ! Undefined
+def: "Primary name of a gene from EcoGene Database." [EDAM:EBI "EMBRACE definition"]
+synonym: "EcoGene primary gene name" EXACT []
+xref: http://www.geneontology.org/doc/GO.xrf_abbs:ECOGENE_G
+is_a: EDAM:0001026 ! Gene symbol
+relationship: is_identifier_of EDAM:0000051 ! Gene
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
-id: EDAM:0002103
-name: KEGG GENES entry name
+id: EDAM:0001787
+name: Gene name (MaizeGDB)
 namespace: data
-def: "Name of an entry from the KEGG GENES database." [EDAM:EBI "EMBRACE definition"]
-xref: Moby_namespace:GeneId
-is_a: EDAM:0001025 ! Gene identifier
-! relationship: is_identifier_of EDAM:0001610 ! KEGG GENES gene report format
+def: "Name of a gene from MaizeGDB (maize genes) database." [EDAM:EBI "EMBRACE definition"]
+xref: http://www.geneontology.org/doc/GO.xrf_abbs:MaizeGDB_Locus
+is_a: EDAM:0001026 ! Gene symbol
+relationship: is_identifier_of EDAM:0000051 ! Gene
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
-
-
-
-
-!
-! Data<-Identifier<-Locus identifier<-Gene identifier<-GeneDB identifier
-!
 [Term]
-id: EDAM:0001797
-name: Glossina morsitans GeneDB gene ID
+id: EDAM:0001788
+name: Gene name (SGD)
 namespace: data
-def: "Gene identifier from Glossina morsitans GeneDB database." [EDAM:EBI "EMBRACE definition"]
-xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Gmorsitans
-is_a: EDAM:0001035 ! GeneDB identifier
+def: "Name of a gene from Saccharomyces Genome Database." [EDAM:EBI "EMBRACE definition"]
+xref: http://www.geneontology.org/doc/GO.xrf_abbs:SGD_LOCUS
+is_a: EDAM:0001026 ! Gene symbol
 relationship: is_identifier_of EDAM:0000051 ! Gene
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
-id: EDAM:0001798
-name: Leishmania major GeneDB gene ID
+id: EDAM:0001789
+name: Gene name (TGD)
 namespace: data
-def: "Gene identifier from Leishmania major GeneDB database." [EDAM:EBI "EMBRACE definition"]
-xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Lmajor
-is_a: EDAM:0001035 ! GeneDB identifier
+def: "Name of a gene from Tetrahymena Genome Database." [EDAM:EBI "EMBRACE definition"]
+xref: http://www.geneontology.org/doc/GO.xrf_abbs:TGD_LOCUS
+is_a: EDAM:0001026 ! Gene symbol
 relationship: is_identifier_of EDAM:0000051 ! Gene
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
-id: EDAM:0001799
-name: Plasmodium falciparum GeneDB gene ID
+id: EDAM:0001790
+name: Gene name (CGSC)
 namespace: data
-def: "Gene identifier from Plasmodium falciparum GeneDB database." [EDAM:EBI "EMBRACE definition"]
-xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Pfalciparum
-is_a: EDAM:0001035 ! GeneDB identifier
+def: "Symbol of a gene from E.coli Genetic Stock Center." [EDAM:EBI "EMBRACE definition"]
+xref: http://www.geneontology.org/doc/GO.xrf_abbs: CGSC
+is_a: EDAM:0001026 ! Gene symbol
 relationship: is_identifier_of EDAM:0000051 ! Gene
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
-id: EDAM:0001800
-name: Schizosaccharomyces pombe GeneDB gene ID
+id: EDAM:0001791
+name: Gene name (HGNC)
+namespace: data
+def: "Symbol of a gene approved by the HUGO Gene Nomenclature Committee." [EDAM:EBI "EMBRACE definition"]
+synonym: "Official gene name" EXACT []
+synonym: "Gene name (HUGO)" EXACT []
+synonym: "HGNC symbol" EXACT []
+synonym: "HUGO symbol" EXACT []
+synonym: "HGNC gene symbol" EXACT []
+synonym: "HUGO gene symbol" EXACT []
+synonym: "HUGO gene name" EXACT []
+synonym: "HGNC gene name" EXACT []
+xref: http://www.geneontology.org/doc/GO.xrf_abbs: HGNC_gene
+is_a: EDAM:0001026 ! Gene symbol
+relationship: is_identifier_of EDAM:0000051 ! Gene
+relationship: is_input_of EDAM:0000223 ! Undefined
+relationship: is_output_of EDAM:0000223 ! Undefined
+relationship: has_source EDAM:0000580 ! Undefined
+
+[Term]
+id: EDAM:0001792
+name: Gene name (MGD)
 namespace: data
-def: "Gene identifier from Schizosaccharomyces pombe GeneDB database." [EDAM:EBI "EMBRACE definition"]
-xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Spombe
-is_a: EDAM:0001035 ! GeneDB identifier
+def: "Symbol of a gene from the Mouse Genome Database." [EDAM:EBI "EMBRACE definition"]
+xref: http://www.geneontology.org/doc/GO.xrf_abbs: MGD
+is_a: EDAM:0001026 ! Gene symbol
 relationship: is_identifier_of EDAM:0000051 ! Gene
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
-id: EDAM:0001801
-name: Trypanosoma brucei GeneDB gene ID
+id: EDAM:0001793
+name: Gene name (Bacillus subtilis)
 namespace: data
-def: "Gene identifier from Trypanosoma brucei GeneDB database." [EDAM:EBI "EMBRACE definition"]
-xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Tbrucei
-is_a: EDAM:0001035 ! GeneDB identifier
+def: "Symbol of a gene from Bacillus subtilis Genome Sequence Project." [EDAM:EBI "EMBRACE definition"]
+xref: http://www.geneontology.org/doc/GO.xrf_abbs: SUBTILISTG
+is_a: EDAM:0001026 ! Gene symbol
 relationship: is_identifier_of EDAM:0000051 ! Gene
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
+[Term]
+id: EDAM:0002103
+name: Gene name (KEGG GENES)
+namespace: data
+def: "Name of an entry (gene) from the KEGG GENES database." [EDAM:EBI "EMBRACE definition"]
+synonym: "KEGG GENES entry name" EXACT []
+xref: Moby_namespace:GeneId
+is_a: EDAM:0001026 ! Gene symbol
+! relationship: is_identifier_of EDAM:0001610 ! KEGG GENES gene report format
+relationship: is_input_of EDAM:0000223 ! Undefined
+relationship: is_output_of EDAM:0000223 ! Undefined
+relationship: has_source EDAM:0000580 ! Undefined
+
+[Term]
+id: EDAM:0002296
+name: Gene name (AceView)
+namespace: data
+def: "Name of an entry (gene) from the AceView genes database." [EDAM:EBI "EMBRACE definition"]
+synonym: "AceView gene name" EXACT []
+is_a: EDAM:0001026 ! Gene symbol
+relationship: is_identifier_of EDAM:0000008 ! Undefined
+relationship: is_input_of EDAM:0000223 ! Undefined
+relationship: is_output_of EDAM:0000223 ! Undefined
+relationship: has_source EDAM:0000580 ! Undefined
+
+[Term]
+id: EDAM:0002300
+name: Gene name (NCBI)
+namespace: data
+def: "Name of an entry (gene) from the NCBI genes database." [EDAM:EBI "EMBRACE definition"]
+synonym: "NCBI gene name" EXACT []
+is_a: EDAM:0001026 ! Gene symbol
+relationship: is_identifier_of EDAM:0000008 ! Undefined
+relationship: is_input_of EDAM:0000223 ! Undefined
+relationship: is_output_of EDAM:0000223 ! Undefined
+relationship: has_source EDAM:0000580 ! Undefined
 
 
 !
-! Data<-Identifier<-Locus identifier<-Gene identifier<-Gene name
+! Data<-Identifier<-Gene identifier<-Gene ID
 !
 [Term]
-id: EDAM:0001806
-name: Gene synonym
+id: EDAM:0001028
+name: Gene identifier (NCBI RefSeq)
 namespace: data
-def: "Any name (other than the recommended one) for a gene." [EDAM:EBI "EMBRACE definition"]
-synonym: "Gene name synonym" EXACT []
-is_a: EDAM:0001026 ! Gene name
-relationship: is_identifier_of EDAM:0000051 ! Gene
+def: "An NCBI RefSeq unique identifier of a gene." [EDAM:EBI "EMBRACE definition"]
+is_obsolete: true
+consider: EDAM:0001027 ! NCBI gene ID
+
+[Term]
+id: EDAM:0001029
+name: Gene identifier (NCBI UniGene)
+namespace: data
+def: "An NCBI UniGene unique identifier of a gene." [EDAM:EBI "EMBRACE definition"]
+is_obsolete: true
+consider: EDAM:0001104 ! UniGene cluster ID
+
+[Term]
+id: EDAM:0001030
+name: Gene identifier (Entrez)
+namespace: data
+def: "An Entrez unique identifier of a gene." [EDAM:EBI "EMBRACE definition"]
+is_obsolete: true
+consider: EDAM:0001027 ! NCBI gene ID
+
+
+[Term]
+id: EDAM:0001886
+name: Blattner number
+namespace: data
+def: "The blattner identifier for a gene." [EDAM:EBI "EMBRACE definition"]
+xref: Moby_namespace:Blattner_number
+is_a: EDAM:0002295 ! Gene ID
+relationship: is_identifier_of EDAM:0000008 ! Undefined
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
-! GeneFarm gene identifier is also given
+
 [Term]
-id: EDAM:0001892
-name: GeneFarm gene name
+id: EDAM:0001027
+name: Gene ID (NCBI)
 namespace: data
-def: "Name of a gene from the GeneFarm database." [EDAM:EBI "EMBRACE definition"]
-xref: Moby_namespace:GENEFARM_GeneName
-is_a: EDAM:0001026 ! Gene name
-relationship: is_identifier_of EDAM:0000051 ! Gene
+def: "An NCBI unique identifier of a gene." [EDAM:EBI "EMBRACE definition"]
+synonym: "Gene identifier (NCBI)" EXACT []
+synonym: "NCBI gene ID" EXACT []
+synonym: "NCBI geneid" EXACT []
+synonym: "Gene identifier (Entrez)" EXACT []
+synonym: "Entrez gene ID" EXACT []
+xref: http://www.geneontology.org/doc/GO.xrf_abbs:NCBI_Gene
+xref: http://www.geneontology.org/doc/GO.xrf_abbs:LocusID
+is_a: EDAM:0002295 ! Gene ID
+! relationship: is_identifier_of EDAM:0001782 ! NCBI gene report format
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
+[Term]
+id: EDAM:0001031
+name: Gene ID (CGD)
+namespace: data
+def: "Identifier of a gene or feature from the CGD database." [EDAM:EBI "EMBRACE definition"]
+synonym: "CGD ID" EXACT []
+is_a: EDAM:0002295 ! Gene ID
+! relationship: is_identifier_of EDAM:0001605 ! CGD gene report format
+relationship: is_input_of EDAM:0000223 ! Undefined
+relationship: is_output_of EDAM:0000223 ! Undefined
+relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
-id: EDAM:0001889
-name: DragonDB gene name
+id: EDAM:0001032
+name: Gene ID (DictyBase)
 namespace: data
-def: "The name of an Antirrhinum Gene from the DragonDB database." [EDAM:EBI "EMBRACE definition"]
-xref: Moby_namespace:DragonDB_Gene
-is_a: EDAM:0001026 ! Gene name
-relationship: is_identifier_of EDAM:0000051 ! Gene
+def: "Identifier of a gene from DictyBase." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0002295 ! Gene ID
+! relationship: is_identifier_of EDAM:0001604 ! DictyBase gene report format
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
+[Term]
+id: EDAM:0001033
+name: Gene ID (Ensembl)
+namespace: data
+def: "Unique identifier for a gene (or other feature) from the Ensembl database." [EDAM:EBI "EMBRACE definition"]
+synonym: "Ensembl Gene ID" EXACT []
+is_a: EDAM:0002295 ! Gene ID
+! relationship: is_identifier_of EDAM:0001603 ! Ensembl gene report format
+relationship: is_input_of EDAM:0000223 ! Undefined
+relationship: is_output_of EDAM:0000223 ! Undefined
+relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
-id: EDAM:0001890
-name: Arabidopsis gene symbol
+id: EDAM:0001034
+name: Gene ID (SGD) 
 namespace: data
-def: "A unique identifier for an Arabidopsis gene, which is an acronym or abbreviation of the gene name." [EDAM:EBI "EMBRACE definition"]
-xref: Moby_namespace:ArabidopsisGeneSymbol
-is_a: EDAM:0001026 ! Gene name
-relationship: is_identifier_of EDAM:0000051 ! Gene
+def: "Identifier of an entry from the SGD database." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0002295 ! Gene ID
+synonym: "SGD identifier" EXACT []
+! relationship: is_identifier_of EDAM:0001614 ! SGD gene report format
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
-id: EDAM:0001807
-name: Gene ORF name
+id: EDAM:0001885
+name: Gene ID (GeneFarm)
 namespace: data
-def: "The name of an open reading frame attributed by a sequencing project." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0001026 ! Gene name
-relationship: is_identifier_of EDAM:0000051 ! Gene
+def: "Identifier of a gene from the GeneFarm database." [EDAM:EBI "EMBRACE definition"]
+xref: Moby_namespace:GENEFARM_GeneID
+is_a: EDAM:0002295 ! Gene ID
+relationship: is_identifier_of EDAM:0000008 ! Undefined
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
-id: EDAM:0001783
-name: ASPGD gene name
+id: EDAM:0001907
+name: Gene ID (KOME)
 namespace: data
-def: "Name of a gene from Aspergillus Genome Database." [EDAM:EBI "EMBRACE definition"]
-xref: http://www.geneontology.org/doc/GO.xrf_abbs:ASPGD_LOCUS
-is_a: EDAM:0001026 ! Gene name
-relationship: is_identifier_of EDAM:0000051 ! Gene
+def: "Identifier of a gene from the KOME database." [EDAM:EBI "EMBRACE definition"]
+xref: Moby_namespace:GeneId
+is_a: EDAM:0002295 ! Gene ID
+relationship: is_identifier_of EDAM:0000008 ! Undefined
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
-id: EDAM:0001784
-name: CGD gene name
+id: EDAM:0001794
+name: Gene ID (PlasmoDB)
 namespace: data
-def: "Name of a gene from Candida Genome Database." [EDAM:EBI "EMBRACE definition"]
-xref: http://www.geneontology.org/doc/GO.xrf_abbs:CGD_LOCUS
-is_a: EDAM:0001026 ! Gene name
+def: "Identifier of a gene from PlasmoDB Plasmodium Genome Resource." [EDAM:EBI "EMBRACE definition"]
+xref: http://www.geneontology.org/doc/GO.xrf_abbs: ApiDB_PlasmoDB
+is_a: EDAM:0002295 ! Gene ID
 relationship: is_identifier_of EDAM:0000051 ! Gene
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
-id: EDAM:0001785
-name: dictyBase gene name
+id: EDAM:0001795
+name: Gene ID (EcoGene)
 namespace: data
-def: "Name of a gene from dictyBase database." [EDAM:EBI "EMBRACE definition"]
-xref: http://www.geneontology.org/doc/GO.xrf_abbs:dictyBase
-is_a: EDAM:0001026 ! Gene name
+def: "Identifier of a gene from EcoGene Database." [EDAM:EBI "EMBRACE definition"]
+synonym: "EcoGene Accession" EXACT []
+synonym: "EcoGene ID" EXACT []
+is_a: EDAM:0002295 ! Gene ID
 relationship: is_identifier_of EDAM:0000051 ! Gene
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
-id: EDAM:0001786
-name: EcoGene primary gene name
+id: EDAM:0002297
+name: Gene ID (ECK)
 namespace: data
-def: "Primary name of a gene from EcoGene Database." [EDAM:EBI "EMBRACE definition"]
-xref: http://www.geneontology.org/doc/GO.xrf_abbs:ECOGENE_G
-is_a: EDAM:0001026 ! Gene name
+def: "Identifier of an E. coli K-12 gene from EcoGene Database." [EDAM:EBI "EMBRACE definition"]
+synonym: "E. coli K-12 gene identifier" EXACT []
+synonym: "ECK accession" EXACT []
+xref: http://www.geneontology.org/doc/GO.xrf_abbs: ECK
+is_a: EDAM:0001795 ! Gene ID (EcoGene)
 relationship: is_identifier_of EDAM:0000051 ! Gene
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
+
+
 [Term]
-id: EDAM:0001787
-name: MaizeGDB gene name
+id: EDAM:0001796
+name: Gene ID (FlyBase)
 namespace: data
-def: "Name of a gene from MaizeGDB (maize genes) database." [EDAM:EBI "EMBRACE definition"]
-xref: http://www.geneontology.org/doc/GO.xrf_abbs:MaizeGDB_Locus
-is_a: EDAM:0001026 ! Gene name
+def: "Gene identifier from FlyBase database." [EDAM:EBI "EMBRACE definition"]
+xref: http://www.geneontology.org/doc/GO.xrf_abbs: FB
+xref: http://www.geneontology.org/doc/GO.xrf_abbs: FlyBase
+is_a: EDAM:0002295 ! Gene ID
 relationship: is_identifier_of EDAM:0000051 ! Gene
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
+
 [Term]
-id: EDAM:0001788
-name: SGD gene name
+id: EDAM:0001802
+name: Gene ID (Gramene)
 namespace: data
-def: "Name of a gene from Saccharomyces Genome Database." [EDAM:EBI "EMBRACE definition"]
-xref: http://www.geneontology.org/doc/GO.xrf_abbs:SGD_LOCUS
-is_a: EDAM:0001026 ! Gene name
+def: "Gene identifier from Gramene database." [EDAM:EBI "EMBRACE definition"]
+xref: http://www.geneontology.org/doc/GO.xrf_abbs: GR_gene
+xref: http://www.geneontology.org/doc/GO.xrf_abbs: GR_GENE
+is_a: EDAM:0002295 ! Gene ID
 relationship: is_identifier_of EDAM:0000051 ! Gene
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
-id: EDAM:0001789
-name: TGD gene name
+id: EDAM:0001803
+name: Gene ID (Virginia microbial)
 namespace: data
-def: "Name of a gene from Tetrahymena Genome Database." [EDAM:EBI "EMBRACE definition"]
-xref: http://www.geneontology.org/doc/GO.xrf_abbs:TGD_LOCUS
-is_a: EDAM:0001026 ! Gene name
+def: "Gene identifier from Virginia Bioinformatics Institute microbial database." [EDAM:EBI "EMBRACE definition"]
+xref: http://www.geneontology.org/doc/GO.xrf_abbs: PAMGO_VMD
+xref: http://www.geneontology.org/doc/GO.xrf_abbs: VMD
+is_a: EDAM:0002295 ! Gene ID
 relationship: is_identifier_of EDAM:0000051 ! Gene
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
-
+[Term]
+id: EDAM:0001804
+name: Gene ID (SGN)
+namespace: data
+def: "Gene identifier from Sol Genomics Network." [EDAM:EBI "EMBRACE definition"]
+xref: http://www.geneontology.org/doc/GO.xrf_abbs: SGN
+is_a: EDAM:0002295 ! Gene ID
+relationship: is_identifier_of EDAM:0000051 ! Gene
+relationship: is_input_of EDAM:0000223 ! Undefined
+relationship: is_output_of EDAM:0000223 ! Undefined
+relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
-id: EDAM:0001790
-name: CGSC gene symbol
+id: EDAM:0001805
+name: Gene ID (WormBase)
 namespace: data
-def: "Symbol of a gene from E.coli Genetic Stock Center." [EDAM:EBI "EMBRACE definition"]
-xref: http://www.geneontology.org/doc/GO.xrf_abbs: CGSC
-is_a: EDAM:0001026 ! Gene name
+def: "Gene identifier used by WormBase database." [EDAM:EBI "EMBRACE definition"]
+xref: http://www.geneontology.org/doc/GO.xrf_abbs: WB
+xref: http://www.geneontology.org/doc/GO.xrf_abbs: WormBase
+is_a: EDAM:0002295 ! Gene ID
+is_a: EDAM:0002113 ! WormBase identifier
 relationship: is_identifier_of EDAM:0000051 ! Gene
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
-id: EDAM:0001791
-name: HUGO gene symbol
+id: EDAM:0001035
+name: Gene ID (GeneDB)
 namespace: data
-def: "Symbol of a gene from HUGO Gene Nomenclature Committee." [EDAM:EBI "EMBRACE definition"]
-xref: http://www.geneontology.org/doc/GO.xrf_abbs: HGNC_gene
-is_a: EDAM:0001026 ! Gene name
-relationship: is_identifier_of EDAM:0000051 ! Gene
+def: "Identifier of a gene from the GeneDB database." [EDAM:EBI "EMBRACE definition"]
+synonym: "GeneDB identifier" EXACT []
+xref: Moby_namespace:GeneDB
+is_a: EDAM:0002295 ! Gene ID
+! relationship: is_identifier_of EDAM:0001615 ! GeneDB entry
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
-id: EDAM:0001792
-name: MGD gene symbol
+id: EDAM:0002285
+name: Gene ID (MIPS)
 namespace: data
-def: "Symbol of a gene from the Mouse Genome Database." [EDAM:EBI "EMBRACE definition"]
-xref: http://www.geneontology.org/doc/GO.xrf_abbs: MGD
-is_a: EDAM:0001026 ! Gene name
-relationship: is_identifier_of EDAM:0000051 ! Gene
+def: "Identifier for genetic elements in MIPS database." [EDAM:EBI "EMBRACE definition"]
+synonym: "MIPS genetic element identifier" EXACT []
+is_a: EDAM:0002295 ! Gene ID
+relationship: is_identifier_of EDAM:0000008 ! Undefined
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
+
 [Term]
-id: EDAM:0001793
-name: Bacillus subtilis gene symbol
+id: EDAM:0002298
+name: Gene ID (HGNC)
 namespace: data
-def: "Symbol of a gene from Bacillus subtilis Genome Sequence Project." [EDAM:EBI "EMBRACE definition"]
-xref: http://www.geneontology.org/doc/GO.xrf_abbs: SUBTILISTG
-is_a: EDAM:0001026 ! Gene name
-relationship: is_identifier_of EDAM:0000051 ! Gene
+def: "Identifier for a gene approved by the HUGO Gene Nomenclature Committee." [EDAM:EBI "EMBRACE definition"]
+synonym: "HGNC ID" EXACT []
+is_a: EDAM:0002295 ! Gene ID
+relationship: is_identifier_of EDAM:0000008 ! Undefined
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
+
+
+!
+! Data<-Identifier<-Gene identifier<-Gene ID (GeneDB)
+!
 [Term]
-id: EDAM:0001794
-name: PlasmoDB gene ID
+id: EDAM:0001797
+name: Gene ID (GeneDB Glossina morsitans)
 namespace: data
-def: "Identifier of a gene from PlasmoDB Plasmodium Genome Resource." [EDAM:EBI "EMBRACE definition"]
-xref: http://www.geneontology.org/doc/GO.xrf_abbs: ApiDB_PlasmoDB
-is_a: EDAM:0001026 ! Gene name
+def: "Gene identifier from Glossina morsitans GeneDB database." [EDAM:EBI "EMBRACE definition"]
+xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Gmorsitans
+is_a: EDAM:0001035 ! Gene ID (GeneDB)
 relationship: is_identifier_of EDAM:0000051 ! Gene
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
-id: EDAM:0001795
-name: ECK accession
+id: EDAM:0001798
+name: Gene ID (GeneDB Leishmania major)
 namespace: data
-def: "Identifier of a gene from EcoGene Database." [EDAM:EBI "EMBRACE definition"]
-synonym: "E. coli K-12 gene identifier" EXACT []
-xref: http://www.geneontology.org/doc/GO.xrf_abbs: ECK
-is_a: EDAM:0001026 ! Gene name
+def: "Gene identifier from Leishmania major GeneDB database." [EDAM:EBI "EMBRACE definition"]
+xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Lmajor
+is_a: EDAM:0001035 ! Gene ID (GeneDB)
 relationship: is_identifier_of EDAM:0000051 ! Gene
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
-id: EDAM:0001796
-name: FlyBase gene ID
+id: EDAM:0001799
+name: Gene ID (GeneDB Plasmodium falciparum)
 namespace: data
-def: "Gene identifier from FlyBase database." [EDAM:EBI "EMBRACE definition"]
-xref: http://www.geneontology.org/doc/GO.xrf_abbs: FB
-xref: http://www.geneontology.org/doc/GO.xrf_abbs: FlyBase
-is_a: EDAM:0001026 ! Gene name
+def: "Gene identifier from Plasmodium falciparum GeneDB database." [EDAM:EBI "EMBRACE definition"]
+xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Pfalciparum
+is_a: EDAM:0001035 ! Gene ID (GeneDB)
 relationship: is_identifier_of EDAM:0000051 ! Gene
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
-
 [Term]
-id: EDAM:0001802
-name: Gramene gene ID
+id: EDAM:0001800
+name: Gene ID (GeneDB Schizosaccharomyces pombe)
 namespace: data
-def: "Gene identifier from Gramene database." [EDAM:EBI "EMBRACE definition"]
-xref: http://www.geneontology.org/doc/GO.xrf_abbs: GR_gene
-xref: http://www.geneontology.org/doc/GO.xrf_abbs: GR_GENE
-is_a: EDAM:0001026 ! Gene name
+def: "Gene identifier from Schizosaccharomyces pombe GeneDB database." [EDAM:EBI "EMBRACE definition"]
+xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Spombe
+is_a: EDAM:0001035 ! Gene ID (GeneDB)
 relationship: is_identifier_of EDAM:0000051 ! Gene
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
-id: EDAM:0001803
-name: Virginia microbial gene ID
+id: EDAM:0001801
+name: Gene ID (GeneDB Trypanosoma brucei)
 namespace: data
-def: "Gene identifier from Virginia Bioinformatics Institute microbial database." [EDAM:EBI "EMBRACE definition"]
-xref: http://www.geneontology.org/doc/GO.xrf_abbs: PAMGO_VMD
-xref: http://www.geneontology.org/doc/GO.xrf_abbs: VMD
-is_a: EDAM:0001026 ! Gene name
+def: "Gene identifier from Trypanosoma brucei GeneDB database." [EDAM:EBI "EMBRACE definition"]
+xref: http://www.geneontology.org/doc/GO.xrf_abbs: GeneDB_Tbrucei
+is_a: EDAM:0001035 ! Gene ID (GeneDB)
 relationship: is_identifier_of EDAM:0000051 ! Gene
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
+
+
+!
+! Data<-Identifier<-Gene identifier<-Gene ID (MIPS)
+!
 [Term]
-id: EDAM:0001804
-name: SGN gene ID
+id: EDAM:0001887
+name: Gene ID (MIPS Maize)
 namespace: data
-def: "Gene identifier from Sol Genomics Network." [EDAM:EBI "EMBRACE definition"]
-xref: http://www.geneontology.org/doc/GO.xrf_abbs: SGN
-is_a: EDAM:0001026 ! Gene name
-relationship: is_identifier_of EDAM:0000051 ! Gene
+def: "Identifier for genetic elements in MIPS Maize database." [EDAM:EBI "EMBRACE definition"]
+synonym: "MIPS genetic element identifier (Maize)" EXACT []
+xref: Moby_namespace:MIPS_GE_Maize
+is_a: EDAM:0002285 ! Gene ID (MIPS)
+relationship: is_identifier_of EDAM:0000008 ! Undefined
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
-id: EDAM:0001805
-name: WormBase gene ID
+id: EDAM:0001888
+name:  Gene ID (MIPS Medicago)
 namespace: data
-def: "Gene identifier used by WormBase database." [EDAM:EBI "EMBRACE definition"]
-xref: http://www.geneontology.org/doc/GO.xrf_abbs: WB
-xref: http://www.geneontology.org/doc/GO.xrf_abbs: WormBase
-is_a: EDAM:0001026 ! Gene name
-is_a: EDAM:0002113 ! WormBase identifier
-is_a: EDAM:0002091 ! Accession
-relationship: is_identifier_of EDAM:0000051 ! Gene
+def: "Identifier for genetic elements in MIPS Medicago database." [EDAM:EBI "EMBRACE definition"]
+synonym: "MIPS genetic element identifier (Medicago)" EXACT []
+xref: Moby_namespace:MIPS_GE_Medicago
+is_a: EDAM:0002285 ! Gene ID (MIPS)
+relationship: is_identifier_of EDAM:0000008 ! Undefined
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
+
+
+
+
+
+
+
+
+
+
+
+
+
 !
 ! Data<-Identifier<-Genetic code identifier
 !
@@ -14717,9 +15288,10 @@ relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
 id: EDAM:0001040
-name: CATH domain identifier
-namespace: data
+name: CATH domain ID
+namespace: data 
 def: "Identifier of a protein domain from CATH." [EDAM:EBI "EMBRACE definition"]
+synonym: "CATH domain identifier" EXACT []
 comment: For example '1nr3A00'.
 is_a: EDAM:0001038 ! Protein domain identifier
 relationship: is_identifier_of EDAM:0000065 ! Protein domain
@@ -14744,9 +15316,11 @@ relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
 id: EDAM:0001042
-name: SCOP unique identifier (sunid)
+name: SCOP sunid
 namespace: data
 def: "Unique identifier (number) of an entry in the SCOP hierarchy, for example 33229." [EDAM:EBI "EMBRACE definition"]
+synonym: "sunid" EXACT []
+synonym: "SCOP unique identifier" EXACT []
 comment: A sunid uniquely identifies an entry in the SCOP hierarchy, including leaves (the SCOP domains) and higher level nodes including entries corresponding to the protein level.
 is_a: EDAM:0001039 ! SCOP domain identifier
 relationship: is_identifier_of EDAM:0001554 ! SCOP classification node
@@ -14915,7 +15489,7 @@ relationship: has_source EDAM:0000580 ! Undefined
 id: EDAM:0001046
 name: Strain name
 namespace: data
-def: "The name of a strain of bacteria." [EDAM:EBI "EMBRACE definition"]
+def: "The name of a strain of an organism variant, typically a plant, virus or bacterium." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0001868 ! Taxon
 relationship: is_identifier_of EDAM:0000072 ! Strain
 relationship: is_input_of EDAM:0000223 ! Undefined
@@ -14923,6 +15497,68 @@ relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
 
+!
+! Data<-Identifier<-Organism identifier<-Taxon<-Strain name
+!
+[Term]
+id: EDAM:0002316
+name: Cell line name
+namespace: data
+def: "The name of a cell line." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0001046 ! Strain name
+relationship: is_identifier_of EDAM:0000072 ! Strain
+relationship: is_input_of EDAM:0000223 ! Undefined
+relationship: is_output_of EDAM:0000223 ! Undefined
+relationship: has_source EDAM:0000580 ! Undefined
+
+
+
+!
+! Data<-Identifier<-Organism identifier<-Taxon<-Strain name<-Cell line name
+!
+[Term]
+id: EDAM:0002317
+name: Cell line name (exact)
+namespace: data
+def: "The name of a cell line." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0002316 ! Cell line name 
+relationship: is_identifier_of EDAM:0000072 ! Strain
+relationship: is_input_of EDAM:0000223 ! Undefined
+relationship: is_output_of EDAM:0000223 ! Undefined
+relationship: has_source EDAM:0000580 ! Undefined
+
+[Term]
+id: EDAM:0002318
+name: Cell line name (truncated)
+namespace: data
+def: "The name of a cell line." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0002316 ! Cell line name 
+relationship: is_identifier_of EDAM:0000072 ! Strain
+relationship: is_input_of EDAM:0000223 ! Undefined
+relationship: is_output_of EDAM:0000223 ! Undefined
+relationship: has_source EDAM:0000580 ! Undefined
+
+[Term]
+id: EDAM:0002319
+name: Cell line name (no punctuation)
+namespace: data
+def: "The name of a cell line." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0002316 ! Cell line name 
+relationship: is_identifier_of EDAM:0000072 ! Strain
+relationship: is_input_of EDAM:0000223 ! Undefined
+relationship: is_output_of EDAM:0000223 ! Undefined
+relationship: has_source EDAM:0000580 ! Undefined
+
+[Term]
+id: EDAM:0002320
+name: Cell line name (assonant)
+namespace: data
+def: "The name of a cell line." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0002316 ! Cell line name 
+relationship: is_identifier_of EDAM:0000072 ! Strain
+relationship: is_input_of EDAM:0000223 ! Undefined
+relationship: is_output_of EDAM:0000223 ! Undefined
+relationship: has_source EDAM:0000580 ! Undefined
 
 
 !
@@ -14979,7 +15615,7 @@ id: EDAM:0001055
 name: LSID
 namespace: data
 def: "A Life Science Identifier (LSID) - a unique identifier of some data." [EDAM:EBI "EMBRACE definition"]
-comment: LSIDs provide a standard way to locate and describe data.  An LSID is represented as a Uniform Resource Name (URN) with the following format: URN:LSID:<Authority>:<Namespace>:<ObjectID>[:<Version>]
+comment: LSIDs provide a standard way to locate and describe data. An LSID is represented as a Uniform Resource Name (URN) with the following format: URN:LSID:<Authority>:<Namespace>:<ObjectID>[:<Version>]
 synonym: "Life Science Identifier" EXACT []
 is_a: EDAM:0001053 ! URN
 relationship: is_identifier_of EDAM:0000008 ! Undefined
@@ -15130,10 +15766,34 @@ relationship: has_identifier EDAM:0000841 ! Undefined
 ! Data<-Identifier<-Sequence identifier
 !
 [Term]
+id: EDAM:0002288
+name: Protein sequence identifier
+namespace: data
+def: "An identifier of protein sequence(s) or protein sequence database entries." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0001063 ! Sequence identifier
+relationship: is_identifier_of EDAM:0002044 ! Sequence data
+relationship: is_identifier_of EDAM:0000849 ! Sequence record
+relationship: is_input_of EDAM:0000223 ! Undefined
+relationship: is_output_of EDAM:0000223 ! Undefined
+relationship: has_source EDAM:0000580 ! Undefined
+
+[Term]
+id: EDAM:0002289
+name: Nucleotide sequence identifier
+namespace: data
+def: "An identifier of nucleotide sequence(s) or nucleotide sequence database entries." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0001063 ! Sequence identifier
+relationship: is_identifier_of EDAM:0002044 ! Sequence data
+relationship: is_identifier_of EDAM:0000849 ! Sequence record
+relationship: is_input_of EDAM:0000223 ! Undefined
+relationship: is_output_of EDAM:0000223 ! Undefined
+relationship: has_source EDAM:0000580 ! Undefined
+
+[Term]
 id: EDAM:0001093
 name: Sequence accession number
 namespace: data
-def: "An accession number or database identifier of an entry from a molecular sequence database." [EDAM:EBI "EMBRACE definition"]
+def: "A persistent, unique identifier of a molecular sequence database entry." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0001063 ! Sequence identifier
 is_a: EDAM:0002091 ! Accession
 relationship: is_identifier_of EDAM:0002044 ! Sequence data
@@ -15142,6 +15802,7 @@ relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
+
 [Term]
 id: EDAM:0002154
 name: Sequence name
@@ -15155,29 +15816,90 @@ relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
+
 [Term]
-id: EDAM:0001094
-name: Sequence type name
+id: EDAM:0001095
+name: EMBOSS Uniform Sequence Address
 namespace: data
-def: "The name of a type of a molecular sequence." [EDAM:EBI "EMBRACE definition"]
-comment: Sequence type might reflect the molecule (protein, nucleic acid etc) or the sequence itself (gapped, ambiguous etc).
+def: "The name of a sequence-based entity adhering to the standard sequence naming scheme used by all EMBOSS applications." [EDAM:EBI "EMBRACE definition"]
+synonym: "USA" EXACT []
 is_a: EDAM:0001063 ! Sequence identifier
-is_a: EDAM:0002100 ! Type
 relationship: is_identifier_of EDAM:0002044 ! Sequence data
 relationship: is_identifier_of EDAM:0000849 ! Sequence record
+relationship: is_identifier_of EDAM:0000863 ! Sequence alignment
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
+
+
+
+!
+! Data<-Identifier<-Sequence identifier<-Protein sequence identifier
+!
 [Term]
-id: EDAM:0001095
-name: EMBOSS Uniform Sequence Address
+id: EDAM:0002291
+name: UniProt ID
 namespace: data
-def: "An EMBOSS Uniform Sequence Address (USA); the standard sequence naming scheme used by all EMBOSS applications." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0001063 ! Sequence identifier
-relationship: is_identifier_of EDAM:0002044 ! Sequence data
+def: "An identifier a UniProt sequence database entry." [EDAM:EBI "EMBRACE definition"]
+synonym: "UniProt identifier" EXACT []
+is_a: EDAM:0002288 ! Protein sequence identifier
+relationship: is_identifier_of EDAM:0000849 ! Sequence record
+relationship: is_input_of EDAM:0000223 ! Undefined
+relationship: is_output_of EDAM:0000223 ! Undefined
+relationship: has_source EDAM:0000580 ! Undefined
+
+[Term]
+id: EDAM:0001100
+name: PIR identifier
+namespace: data
+def: "An identifier of PIR sequence database entry." [EDAM:EBI "EMBRACE definition"]
+synonym: "PIR accession number" EXACT []
+synonym: "PIR ID" EXACT []
+is_a: EDAM:0002288 ! Protein sequence identifier
+relationship: is_identifier_of EDAM:0000849 ! Sequence record
+relationship: is_input_of EDAM:0000223 ! Undefined
+relationship: is_output_of EDAM:0000223 ! Undefined
+relationship: has_source EDAM:0000580 ! Undefined
+
+[Term]
+id: EDAM:0001101
+name: TREMBL identifier
+namespace: data
+def: "Identifier of a TREMBL sequence database entry." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0001099 ! UniProt accession number
+synonym: "TREMBL accession number" EXACT []
+synonym: "TREMBL ID" EXACT []
+relationship: is_identifier_of EDAM:0000849 ! Sequence record
+relationship: is_input_of EDAM:0000223 ! Undefined
+relationship: is_output_of EDAM:0000223 ! Undefined
+relationship: has_source EDAM:0000580 ! Undefined
+
+
+
+!
+! Data<-Identifier<-Sequence identifier<-Nucleotide sequence identifier
+!
+[Term]
+id: EDAM:0002290
+name: EMBL identifier
+namespace: data
+def: "An identifier of an entry from the EMBL sequence database." [EDAM:EBI "EMBRACE definition"]
+synonym: "EMBL ID" EXACT []
+is_a: EDAM:0002289 ! Nucleotide sequence identifier
+relationship: is_identifier_of EDAM:0000849 ! Sequence record
+relationship: is_input_of EDAM:0000223 ! Undefined
+relationship: is_output_of EDAM:0000223 ! Undefined
+relationship: has_source EDAM:0000580 ! Undefined
+
+[Term]
+id: EDAM:0002292
+name: GenBank identifier
+namespace: data
+def: "An identifier of an entry from the GenBank sequence database." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0002289 ! Nucleotide sequence identifier
+synonym: "GenBank ID" EXACT []
 relationship: is_identifier_of EDAM:0000849 ! Sequence record
-relationship: is_identifier_of EDAM:0000863 ! Sequence alignment
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
@@ -15185,10 +15907,10 @@ relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
 id: EDAM:0001855
-name: Clone identifier
+name: Clone ID
 namespace: data
-def: "An identifier of a clone (a cloned molecular sequence from a database)." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0001063 ! Sequence identifier
+def: "An identifier of a clone (cloned molecular sequence) from a database." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0002289 ! Nucleotide sequence identifier
 relationship: is_identifier_of EDAM:0002044 ! Sequence data
 relationship: is_identifier_of EDAM:0000849 ! Sequence record
 relationship: is_input_of EDAM:0000223 ! Undefined
@@ -15196,6 +15918,27 @@ relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
 
+[Term]
+id: EDAM:0001105
+name: dbEST identifier
+namespace: data
+def: "Identifier of a dbEST database entry." [EDAM:EBI "EMBRACE definition"]
+synonym: "dbEST ID" EXACT []
+is_a: EDAM:0002289 ! Nucleotide sequence identifier
+! relationship: is_identifier_of EDAM:0001229 ! dbEST nucleotide sequence record
+relationship: is_input_of EDAM:0000223 ! Undefined
+relationship: is_output_of EDAM:0000223 ! Undefined
+relationship: has_source EDAM:0000580 ! Undefined
+
+!
+! Data<-Identifier<-Sequence identifier<-Nucleotide sequence identifier<-EMBL identifier
+!
+
+
+
+
+
+
 
 !
 ! Data<-Identifier<-Sequence identifier<-Sequence accession number
@@ -15204,8 +15947,9 @@ relationship: has_source EDAM:0000580 ! Undefined
 id: EDAM:0001096
 name: Protein sequence accession number
 namespace: data
-def: "An accession number or database identifier of an entry from a protein sequence database." [EDAM:EBI "EMBRACE definition"]
+def: "Accession number of a protein sequence database entry." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0001093 ! Sequence accession number
+is_a: EDAM:0002288 ! Protein sequence identifier
 relationship: is_identifier_of EDAM:0001208 ! Protein sequence
 relationship: is_identifier_of EDAM:0000849 ! Sequence record
 relationship: is_input_of EDAM:0000223 ! Undefined
@@ -15216,8 +15960,9 @@ relationship: has_source EDAM:0000580 ! Undefined
 id: EDAM:0001097
 name: Nucleotide sequence accession number
 namespace: data
-def: "An accession number or database identifier of an entry from a nucleotide sequence database." [EDAM:EBI "EMBRACE definition"]
+def: "Accession number of a nucleotide sequence database entry." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0001093 ! Sequence accession number
+is_a: EDAM:0002289 ! Nucleotide sequence identifier
 relationship: is_identifier_of EDAM:0001207 ! Nucleotide sequence
 relationship: is_identifier_of EDAM:0000849 ! Sequence record
 relationship: is_input_of EDAM:0000223 ! Undefined
@@ -15228,13 +15973,52 @@ relationship: has_source EDAM:0000580 ! Undefined
 id: EDAM:0001098
 name: RefSeq accession number
 namespace: data
-def: "Accession number of an entry from the RefSeq database." [EDAM:EBI "EMBRACE definition"]
+def: "Accession number of a RefSeq database entry." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0001093 ! Sequence accession number
+! relationship: is_identifier_of EDAM:0001224 ! RefSeq sequence record
+relationship: is_input_of EDAM:0000223 ! Undefined
+relationship: is_output_of EDAM:0000223 ! Undefined
+relationship: has_source EDAM:0000580 ! Undefined
+
+[Term]
+id: EDAM:0002314
+name: GI number
+namespace: data
+def: "A series of digits that are assigned consecutively to each sequence record processed by NCBI. The GI number bears no resemblance to the Accession number of the sequence record." [EDAM:EBI "EMBRACE definition"]
+comment: Nucleotide sequence GI number is shown in the VERSION field of the database record. Protein sequence GI number is shown in the CDS/db_xref field of a nucleotide database record, and the VERSION field of a protein database record.
+synonym: "NCBI GI number" EXACT []
+synonym: "gi number" EXACT []
+is_a: EDAM:0001093 ! Sequence accession number
+! relationship: is_identifier_of EDAM:0001224 ! RefSeq sequence record
+relationship: is_input_of EDAM:0000223 ! Undefined
+relationship: is_output_of EDAM:0000223 ! Undefined
+relationship: has_source EDAM:0000580 ! Undefined
+
+
+
+
+
+[Term]
+id: EDAM:0002315
+name: NCBI version
+namespace: data
+def: "An identifier assigned to sequence records processed by NCBI, made of the accession number of the database record followed by a dot and a version number." [EDAM:EBI "EMBRACE definition"]
+comment: Nucleotide sequence version contains two letters followed by six digits, a dot, and a version number (or for older nucleotide sequence records, the format is one letter followed by five digits, a dot, and a version number). Protein sequence version contains three letters followed by five digits, a dot, and a version number
+synonym: "accession.version" EXACT []
+synonym: "NCBI accession.version" EXACT []
 is_a: EDAM:0001093 ! Sequence accession number
 ! relationship: is_identifier_of EDAM:0001224 ! RefSeq sequence record
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
+
+
+
+
+
+
+
 !
 ! Data<-Identifier<-Sequence identifier<-Sequence accession number<-Protein sequence accession number
 !
@@ -15242,12 +16026,11 @@ relationship: has_source EDAM:0000580 ! Undefined
 id: EDAM:0001099
 name: UniProt accession number
 namespace: data
-def: "Accession number or database identifier of a protein sequence from UniProt." [EDAM:EBI "EMBRACE definition"]
+def: "Accession number of a UniProt (protein sequence) database entry." [EDAM:EBI "EMBRACE definition"]
 synonym: "UniProt accession" EXACT []
-synonym: "UniProt identifier" EXACT []
-synonym: "UniProt id" EXACT []
 synonym: "SwissProt accession" EXACT []
 is_a: EDAM:0001096 ! Protein sequence accession number
+is_a: EDAM:0002291 ! UniProt identifier
 relationship: is_identifier_of EDAM:0001208 ! Protein sequence
 relationship: is_identifier_of EDAM:0000849 ! Sequence record
 relationship: is_input_of EDAM:0000223 ! Undefined
@@ -15255,39 +16038,32 @@ relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
-id: EDAM:0001100
-name: PIR accession number
+id: EDAM:0001102
+name: Gramene primary identifier
 namespace: data
-def: "Identifier of an entry from the PIR database." [EDAM:EBI "EMBRACE definition"]
+def: "Primary identifier of a Gramene database entry." [EDAM:EBI "EMBRACE definition"]
+synonym: "Gramene primary ID" EXACT []
 is_a: EDAM:0001096 ! Protein sequence accession number
-relationship: is_identifier_of EDAM:0001208 ! Protein sequence
-! relationship: is_identifier_of EDAM:0001232 ! PIR protein sequence record
+! relationship: is_identifier_of EDAM:0001609 ! Gramene entry
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
-id: EDAM:0001101
-name: TREMBL identifier
+id: EDAM:0002293
+name: Gramene secondary identifier
 namespace: data
-def: "Identifier of an entry from the TREMBL database." [EDAM:EBI "EMBRACE definition"]
+def: "Secondary (internal) identifier of a Gramene database entry." [EDAM:EBI "EMBRACE definition"]
+synonym: "Gramene secondary ID" EXACT []
+synonym: "Gramene internal ID" EXACT []
+synonym: "Gramene internal identifier" EXACT []
 is_a: EDAM:0001096 ! Protein sequence accession number
-! relationship: is_identifier_of EDAM:0001231 ! TREMBL protein sequence record
+! relationship: is_identifier_of EDAM:0001609 ! Gramene entry
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
 
-[Term]
-id: EDAM:0001102
-name: Gramene primary identifier
-namespace: data
-def: "Identifier of an entry from the Gramene primary database." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0001096 ! Protein sequence accession number
-! relationship: is_identifier_of EDAM:0001609 ! Gramene entry
-relationship: is_input_of EDAM:0000223 ! Undefined
-relationship: is_output_of EDAM:0000223 ! Undefined
-relationship: has_source EDAM:0000580 ! Undefined
 
 
 !
@@ -15307,27 +16083,7 @@ relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
 
-[Term]
-id: EDAM:0001105
-name: dbEST identifier
-namespace: data
-def: "Identifier of an entry from the dbEST database." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0001097 ! Nucleotide sequence accession number
-! relationship: is_identifier_of EDAM:0001229 ! dbEST nucleotide sequence record
-relationship: is_input_of EDAM:0000223 ! Undefined
-relationship: is_output_of EDAM:0000223 ! Undefined
-relationship: has_source EDAM:0000580 ! Undefined
 
-[Term]
-id: EDAM:0001106
-name: dbSNP identifier
-namespace: data
-def: "Identifier of an entry from the dbSNP database." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0001097 ! Nucleotide sequence accession number
-! relationship: is_identifier_of EDAM:0001620 ! dbSNP polymorphism report format
-relationship: is_input_of EDAM:0000223 ! Undefined
-relationship: is_output_of EDAM:0000223 ! Undefined
-relationship: has_source EDAM:0000580 ! Undefined
 
 !
 ! Data<-Identifier<-Sequence identifier<-Sequence accession number<-Nucleotide sequence accession number<-EMBL/GenBank/DDBJ accession number
@@ -15336,8 +16092,9 @@ relationship: has_source EDAM:0000580 ! Undefined
 id: EDAM:0001107
 name: EMBL accession number
 namespace: data
-def: "Accession number or database identifier of a sequence from the EMBL database." [EDAM:EBI "EMBRACE definition"]
+def: "Accession number of an EMBL sequence database entry." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0001103 ! EMBL/GenBank/DDBJ accession number
+is_a: EDAM:0002290 ! EMBL identifier
 ! relationship: is_identifier_of EDAM:0001226 ! EMBL nucleotide sequence record
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
@@ -15347,21 +16104,20 @@ relationship: has_source EDAM:0000580 ! Undefined
 id: EDAM:0001108
 name: GenBank accession number
 namespace: data
-def: "Accession number or database identifier of a sequence from the GenBank database." [EDAM:EBI "EMBRACE definition"]
+def: "Accession number of a GenBank sequence database entry." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0001103 ! EMBL/GenBank/DDBJ accession number
-is_a: EDAM:0001096 ! Protein sequence accession number
+is_a: EDAM:0002292 ! GenBank identifier
 ! relationship: is_identifier_of EDAM:0001227 ! GenBank nucleotide sequence record
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
 
-
 [Term]
 id: EDAM:0001109
 name: DDBJ accession number
 namespace: data
-def: "Accession number or database identifier of a sequence from the DDBJ database." [EDAM:EBI "EMBRACE definition"]
+def: "Accession number of a DDBJ sequence database entry." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0001103 ! EMBL/GenBank/DDBJ accession number
 ! relationship: is_identifier_of EDAM:0001225 ! DDBJ nucleotide sequence record
 relationship: is_input_of EDAM:0000223 ! Undefined
@@ -15373,9 +16129,53 @@ relationship: has_source EDAM:0000580 ! Undefined
 ! Data<-Identifier<-Sequence identifier<-Sequence accession number<-RefSeq accession number
 !
 
+!
+! Data<-Identifier<-Sequence identifier<-Sequence accession number<-GI number
+!
+[Term]
+id: EDAM:0002327
+name: Protein GI number
+namespace: data
+def: "A unique identifier assigned to NCBI protein sequence records." [EDAM:EBI "EMBRACE definition"]
+comment: Nucleotide sequence GI number is shown in the VERSION field of the database record. Protein sequence GI number is shown in the CDS/db_xref field of a nucleotide database record, and the VERSION field of a protein database record.
+synonym: "protein gi number" EXACT []
+synonym: "protein gi" EXACT []
+is_a: EDAM:0002314 ! GI number
+! relationship: is_identifier_of EDAM:0001224 ! RefSeq sequence record
+relationship: is_input_of EDAM:0000223 ! Undefined
+relationship: is_output_of EDAM:0000223 ! Undefined
+relationship: has_source EDAM:0000580 ! Undefined
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+
+!
+! Data<-Identifier<-Sequence identifier<-Clone ID
+!
+
+
+
+
+
 
 !
-! Data<-Identifier<-Sequence identifier<-Sequence type name
+! Data<-Identifier<-Sequence type name
 !
 [Term]
 id: EDAM:0001110
@@ -15396,8 +16196,22 @@ relationship: has_source EDAM:0000580 ! Undefined
 
 
 !
-! Data<-Identifier<-Sequence identifier<-Clone identifier
+! Data<-Identifier<-Sequence variation identifier
 !
+[Term]
+id: EDAM:0001106
+name: dbSNP identifier
+namespace: data
+def: "Identifier of a dbSNP database entry." [EDAM:EBI "EMBRACE definition"]
+synonym: "dbSNP ID" EXACT []
+is_a: EDAM:0002294 ! Sequence variation identifier
+! relationship: is_identifier_of EDAM:0001620 ! dbSNP polymorphism report format
+relationship: is_input_of EDAM:0000223 ! Undefined
+relationship: is_output_of EDAM:0000223 ! Undefined
+relationship: has_source EDAM:0000580 ! Undefined
+
+
+
 
 
 !
@@ -15668,7 +16482,7 @@ id: EDAM:0001126
 name: Comparison matrix name
 namespace: data
 def: "Unique name or identifier of a comparison matrix." [EDAM:EBI "EMBRACE definition"]
-comment: See for example http://www.ebi.ac.uk/Tools/webservices/help/matrix
+comment: See for example http://www.ebi.ac.uk/Tools/webservices/help/matrix.
 synonym: "Substitution matrix name" EXACT []
 is_a: EDAM:0001069 ! Comparison matrix identifier
 is_a: EDAM:0002099 ! Name
@@ -15746,6 +16560,19 @@ relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
 
+[Term]
+id: EDAM:0002302
+name: STRING ID
+namespace: data
+def: "Unique identifier of an entry from the STRING database of protein-protein interactions." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0001074 ! Protein interaction identifier
+is_a: EDAM:0002091 ! Accession
+! relationship: is_identifier_of EDAM:0001569 ! IntAct entry format
+relationship: is_input_of EDAM:0000223 ! Undefined
+relationship: is_output_of EDAM:0000223 ! Undefined
+relationship: has_source EDAM:0000580 ! Undefined
+
+
 
 !
 ! Data<-Identifier<-Codon usage table identifier
@@ -16201,13 +17028,25 @@ id: EDAM:0001163
 name: MIRIAM data type name
 namespace: data
 def: "The name of a data type from the MIRIAM database." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0001084 ! Data definition identifier
+is_a: EDAM:0002253 ! Data type name
 is_a: EDAM:0002099 ! Name
 relationship: is_identifier_of EDAM:0001664 ! MIRIAM datatype
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
+[Term]
+id: EDAM:0002253
+name: Data type name
+namespace: data
+def: "The name of a data type." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0001084 ! Data definition identifier
+is_a: EDAM:0002099 ! Name
+relationship: is_identifier_of EDAM:0000008 ! Undefined
+relationship: is_input_of EDAM:0000223 ! Undefined
+relationship: is_output_of EDAM:0000223 ! Undefined
+relationship: has_source EDAM:0000580 ! Undefined
+
 
 [Term]
 id: EDAM:0001164
@@ -16277,6 +17116,17 @@ relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
+[Term]
+id: EDAM:0002309
+name: SABIO-RK reaction ID
+namespace: data
+def: "Identifier of a biological reaction from the SABIO-RK reactions database." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0002108 ! Reaction identifier
+relationship: is_identifier_of EDAM:0000008 ! Undefined
+relationship: is_input_of EDAM:0000223 ! Undefined
+relationship: is_output_of EDAM:0000223 ! Undefined
+relationship: has_source EDAM:0000580 ! Undefined
+
 !
 ! Data<-Identifier<-Workflow identifier
 !
@@ -16359,9 +17209,10 @@ relationship: has_source EDAM:0000580 ! Undefined
 
 [Term]
 id: EDAM:0001176
-name: GO term identifier
+name: GO term ID
 namespace: data
 def: "A term from The Gene Ontology." [EDAM:EBI "EMBRACE definition"]
+synonym: "GO term identifier" EXACT []
 is_a: EDAM:0001087 ! Ontology term identifier
 relationship: is_identifier_of EDAM:0001716 ! GO term
 relationship: is_input_of EDAM:0000223 ! Undefined
@@ -16587,6 +17438,20 @@ relationship: has_source EDAM:0000580 ! Undefined
 
 
 
+!
+! Data<-Identifier<-File format name
+!
+[Term]
+id: EDAM:0002254
+name: OBO file format name
+namespace: data
+def: "Name of an OBO file format such as OBO-XML, plain and so on." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0002129 ! File format name
+relationship: is_identifier_of EDAM:0000008 ! Undefined
+relationship: is_input_of EDAM:0000223 ! Undefined
+relationship: is_output_of EDAM:0000223 ! Undefined
+relationship: has_source EDAM:0000580 ! Undefined
+
 
 
 
@@ -16671,6 +17536,56 @@ relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
 
 
+!
+! Data<-Schema
+!
+[Term]
+id: EDAM:0002249
+name: DTD
+namespace: data
+def: "A DTD (document type definition)." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0002248 ! Schema
+relationship: is_attribute_of EDAM:0000008 ! Undefined
+relationship: is_input_of EDAM:0000223 ! Undefined
+relationship: is_output_of EDAM:0000223 ! Undefined
+relationship: has_source EDAM:0000580 ! Undefined
+relationship: has_identifier EDAM:0000841 ! Undefined
+
+[Term]
+id: EDAM:0002250
+name: XSD schema
+namespace: data
+def: "An XSD schema." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0002248 ! Schema
+relationship: is_attribute_of EDAM:0000008 ! Undefined
+relationship: is_input_of EDAM:0000223 ! Undefined
+relationship: is_output_of EDAM:0000223 ! Undefined
+relationship: has_source EDAM:0000580 ! Undefined
+relationship: has_identifier EDAM:0000841 ! Undefined
+
+[Term]
+id: EDAM:0002251
+name: Relax-NG schema
+namespace: data
+def: "A relax-NG schema." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0002248 ! Schema
+relationship: is_attribute_of EDAM:0000008 ! Undefined
+relationship: is_input_of EDAM:0000223 ! Undefined
+relationship: is_output_of EDAM:0000223 ! Undefined
+relationship: has_source EDAM:0000580 ! Undefined
+relationship: has_identifier EDAM:0000841 ! Undefined
+
+[Term]
+id: EDAM:0002252
+name: XSLT stylesheet
+namespace: data
+def: "An XSLT stylesheet." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0002248 ! Schema
+relationship: is_attribute_of EDAM:0000008 ! Undefined
+relationship: is_input_of EDAM:0000223 ! Undefined
+relationship: is_output_of EDAM:0000223 ! Undefined
+relationship: has_source EDAM:0000580 ! Undefined
+relationship: has_identifier EDAM:0000841 ! Undefined
 
 
 !
@@ -16856,6 +17771,17 @@ relationship: has_identifier EDAM:0001061 ! QSAR descriptor name
 !
 ! Data<-General molecular property<-Chemical formula
 !
+[Term]
+id: EDAM:0002301
+name: SMILES string
+namespace: data
+def: "A specification of a chemical structure in SMILES format." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0000846 ! Chemical formula
+relationship: is_attribute_of EDAM:0000013 ! Molecular entity
+relationship: is_input_of EDAM:0000223 ! Undefined
+relationship: is_output_of EDAM:0000223 ! Undefined
+relationship: has_source EDAM:0000580 ! Undefined
+relationship: has_identifier EDAM:0000841 ! Undefined
 
 
 
@@ -17362,7 +18288,7 @@ consider: EDAM:0001929 ! fasta sequence format
 id: EDAM:0001224
 name: RefSeq sequence record
 namespace: data
-def: "A record from RefSeq or any file in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "A record from RefSeq." [EDAM:EBI "EMBRACE definition"]
 is_obsolete: true
 consider: EDAM:0000849 ! Sequence record
 consider: EDAM:0001958 ! refseqp sequence format
@@ -17380,7 +18306,7 @@ consider: EDAM:0001958 ! refseqp sequence format
 id: EDAM:0001225
 name: DDBJ nucleotide sequence record
 namespace: data
-def: "An entry from DDBJ or any file in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "An entry from DDBJ." [EDAM:EBI "EMBRACE definition"]
 is_obsolete: true
 consider: EDAM:0000849 ! Sequence record
 consider: EDAM:0001936 ! genbank sequence format
@@ -17391,7 +18317,7 @@ consider: EDAM:0001936 ! genbank sequence format
 id: EDAM:0001226
 name: EMBL nucleotide sequence record
 namespace: data
-def: "An entry from EMBL or any file in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "An entry from EMBL." [EDAM:EBI "EMBRACE definition"]
 is_obsolete: true
 consider: EDAM:0000849 ! Sequence record
 consider: EDAM:0001936 ! genbank sequence format
@@ -17403,7 +18329,7 @@ consider: EDAM:0001936 ! genbank sequence format
 id: EDAM:0001227
 name: GenBank nucleotide sequence record
 namespace: data
-def: "An entry from GenBank or any file in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "An entry from GenBank." [EDAM:EBI "EMBRACE definition"]
 is_obsolete: true
 consider: EDAM:0000849 ! Sequence record
 consider: EDAM:0001936 ! genbank sequence format
@@ -17427,7 +18353,7 @@ consider: EDAM:0001936 ! genbank sequence format
 id: EDAM:0001229
 name: dbEST nucleotide sequence record
 namespace: data
-def: "An entry from dbEST or any file in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "An entry from dbEST." [EDAM:EBI "EMBRACE definition"]
 is_obsolete: true
 consider: EDAM:0000849 ! Sequence record
 consider: EDAM:0001936 ! genbank sequence format
@@ -17447,7 +18373,7 @@ consider: EDAM:0001936 ! genbank sequence format
 id: EDAM:0001230
 name: UniProt protein sequence record
 namespace: data
-def: "An entry from UniProt/SwissProt or any file in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "An entry from UniProt/SwissProt." [EDAM:EBI "EMBRACE definition"]
 synonym: "SwissProt entry" EXACT []
 is_obsolete: true
 consider: EDAM:0000849 ! Sequence record
@@ -17460,7 +18386,7 @@ consider: EDAM:0001963 ! swiss sequence format
 id: EDAM:0001231
 name: TREMBL protein sequence record
 namespace: data
-def: "An entry from TREMBL or any file in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "An entry from TREMBL." [EDAM:EBI "EMBRACE definition"]
 is_obsolete: true
 consider: EDAM:0000849 ! Sequence record
 consider: EDAM:0001963 ! swiss sequence format
@@ -17472,7 +18398,7 @@ consider: EDAM:0001963 ! swiss sequence format
 id: EDAM:0001232
 name: PIR protein sequence record
 namespace: data
-def: "An entry from PIR or any file in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "An entry from PIR." [EDAM:EBI "EMBRACE definition"]
 synonym: "NBRF format" EXACT []
 is_obsolete: true
 consider: EDAM:0000849 ! Sequence record
@@ -17688,7 +18614,7 @@ consider: EDAM:0000850 ! Sequence set
 id: EDAM:0001244
 name: primersearch primer pairs sequence record
 namespace: data
-def: "File of one or more pairs of primer sequences, as used by EMBOSS primersearch application, or any file in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "File of one or more pairs of primer sequences, as used by EMBOSS primersearch application,." [EDAM:EBI "EMBRACE definition"]
 is_obsolete: true
 consider: EDAM:0000850 ! Sequence set
 
@@ -17891,7 +18817,7 @@ id: EDAM:0001280
 name: DNA physical map
 namespace: data
 def: "A map of DNA (linear or circular) annotated with physical features or landmarks such as restriction sites, cloned DNA fragments, genes or genetic markers, along with the physical distances between them." [EDAM:EBI "EMBRACE definition"]
-comment: Distance in a physical map is measured in base pairs.  A physical map might be ordered relative to a reference map (typically a genetic map) in the process of genome sequencing.
+comment: Distance in a physical map is measured in base pairs. A physical map might be ordered relative to a reference map (typically a genetic map) in the process of genome sequencing.
 is_a: EDAM:0001274 ! Map
 relationship: is_attribute_of EDAM:0000008 ! Undefined
 relationship: is_input_of EDAM:0000223 ! Undefined
@@ -18097,7 +19023,7 @@ name: Sequence complexity
 namespace: data
 def: "A report on sequence complexity, for example low-complexity or repeat regions in sequences." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0001254 ! Sequence property
-relationship: is_attribute_of EDAM:0000008 ! Undefined
+relationship: is_concern_of EDAM:0002263 ! Sequence complexity
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
@@ -18275,7 +19201,7 @@ name: DAS sequence feature annotation
 namespace: data
 def: "Annotation of a molecular sequence in DAS format." [EDAM:EBI "EMBRACE definition"]
 is_obsolete: true
-consider: EDAM:0001978 ! dasgff feature format
+consider: EDAM:0001978 ! dasgff feature
 
 
 
@@ -18462,7 +19388,7 @@ namespace: data
 def: "Location of short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences." [EDAM:EBI "EMBRACE definition"]
 comment: The report might include derived data map such as classification, annotation, organization, periodicity etc.
 is_a: EDAM:0001276 ! Nucleotide sequence feature report
-relationship: is_attribute_of EDAM:0000008 ! Undefined
+relationship: is_concern_of EDAM:0002262 ! Repeat sequences
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
@@ -18496,7 +19422,7 @@ id: EDAM:0001290
 name: InterPro compact match image
 namespace: data
 def: "Image showing matches between protein sequence(s) and InterPro Entries." [EDAM:EBI "EMBRACE definition"]
-comment: The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself.  Each protein is represented as a scaled horizontal line with colored bars indicating the position of the matches.
+comment: The sequence(s) might be screened against InterPro, or be the sequences from the InterPro entry itself. Each protein is represented as a scaled horizontal line with colored bars indicating the position of the matches.
 is_a: EDAM:0001281 ! Sequence signature map
 relationship: is_attribute_of EDAM:0000008 ! Undefined
 relationship: is_input_of EDAM:0000223 ! Undefined
@@ -18684,7 +19610,7 @@ namespace: data
 def: "Image of short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0001299 ! Repeat sequence report
 is_a: EDAM:0000965 ! Image
-relationship: is_attribute_of EDAM:0000008 ! Undefined
+relationship: is_concern_of EDAM:0002262 ! Repeat sequences
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
@@ -20602,7 +21528,7 @@ relationship: has_identifier EDAM:0000841 ! Undefined
 ! Data<-Phylogenetic tree
 !
 [Term]
-id: EDAM:0002245
+id: EDAM:0002247
 name: Phylogenetic consensus tree
 namespace: data
 def: "An informative report on a consensus phylogenetic tree derived from comparison of multiple trees." [EDAM:EBI "EMBRACE definition"]
@@ -21525,7 +22451,7 @@ name: Amino acid
 namespace: data
 def: "An informative report about a specific amino acid." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002016 ! Amino acid data
-is_a: EDAM:0000962 ! Chemical compound
+is_a: EDAM:0000962 ! Chemical compound annotation
 relationship: is_attribute_of EDAM:0000008 ! Undefined
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
@@ -21641,6 +22567,7 @@ id: EDAM:0001509
 name: Enzyme annotation
 namespace: data
 def: "Report on a specific enzyme." [EDAM:EBI "EMBRACE definition"]
+synonym: "Enzyme report" EXACT []
 is_a: EDAM:0000896 ! Protein annotation
 relationship: is_attribute_of EDAM:0000008 ! Undefined
 relationship: is_input_of EDAM:0000223 ! Undefined
@@ -21675,7 +22602,7 @@ relationship: is_attribute_of EDAM:0000008 ! Undefined
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000821 ! Enzyme data resource
-relationship: has_identifier EDAM:0001011 ! Enzyme Commission number
+relationship: has_identifier EDAM:0001011 ! EC number
 
 
 
@@ -21693,7 +22620,7 @@ relationship: is_attribute_of EDAM:0000008 ! Undefined
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000821 ! Enzyme data resource
-relationship: has_identifier EDAM:0001011 ! Enzyme Commission number
+relationship: has_identifier EDAM:0001011 ! EC number
 
 [Term]
 id: EDAM:0001518
@@ -21705,7 +22632,7 @@ relationship: is_attribute_of EDAM:0000008 ! Undefined
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000821 ! Enzyme data resource
-relationship: has_identifier EDAM:0001011 ! Enzyme Commission number
+relationship: has_identifier EDAM:0001011 ! EC number
 
 
 
@@ -21988,7 +22915,7 @@ id: EDAM:0001534
 name: Peptide immunogenicity report
 namespace: data
 def: "An report on allergenicity / immunogenicity of peptides and proteins." [EDAM:EBI "EMBRACE definition"]
-comment: This includes data on peptide ligands that elicit an immune response (immunogens), allergic cross-reactivity, predicted antigenicity (Hopp and Woods plot) etc.  These data are useful in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data.
+comment: This includes data on peptide ligands that elicit an immune response (immunogens), allergic cross-reactivity, predicted antigenicity (Hopp and Woods plot) etc. These data are useful in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data.
 is_a: EDAM:0000897 ! Protein physicochemical property
 relationship: is_attribute_of EDAM:0000008 ! Undefined
 relationship: is_input_of EDAM:0000223 ! Undefined
@@ -22166,9 +23093,10 @@ relationship: has_identifier EDAM:0001043 ! CATH node identifier
 
 [Term]
 id: EDAM:0001554
-name: SCOP classification node
+name: SCOP node
 namespace: data
 def: "Information on a node from the SCOP database, or any report in the same format." [EDAM:EBI "EMBRACE definition"]
+synonym: "SCOP classification node" EXACT []
 is_a: EDAM:0000900 ! Protein domain classification
 relationship: is_attribute_of EDAM:0000065 ! Protein domain
 relationship: is_input_of EDAM:0000223 ! Undefined
@@ -22382,7 +23310,7 @@ relationship: has_identifier EDAM:0000841 ! Undefined
 id: EDAM:0002026
 name: Hanes Woolf plot
 namespace: data
-def: "A plot based on the Michaelis–Menten equation of enzyme kinetics plotting the ratio of the initial substrate concentration (S) against the reaction velocity (v)." [EDAM:EBI "EMBRACE definition"]
+def: "A plot based on the Michaelis Menten equation of enzyme kinetics plotting the ratio of the initial substrate concentration (S) against the reaction velocity (v)." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002024 ! Enzyme kinetics data
 relationship: is_attribute_of EDAM:0000008 ! Undefined
 relationship: is_input_of EDAM:0000223 ! Undefined
@@ -23606,7 +24534,6 @@ name: Biological pathway map
 namespace: data
 def: "A map (typically a diagram) of a biological pathway." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000946 ! Biological pathway
-is_a: EDAM:0000965 ! Image
 relationship: is_attribute_of EDAM:0000008 ! Undefined
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
@@ -23623,7 +24550,7 @@ relationship: has_identifier EDAM:0001082 ! Biological pathway identifier
 id: EDAM:0001656
 name: Metabolic pathway map
 namespace: data
-def: "A map (typically a diagram) of a metabolic pathway." [EDAM:EBI "EMBRACE definition"]
+def: "A report including a map (typically a diagram) of a metabolic pathway." [EDAM:EBI "EMBRACE definition"]
 comment: This includes carbohydrate, energy, lipid, nucleotide, amino acid, glycan, PK/NRP, cofactor/vitamin, secondary metabolite, xenobiotics etc.
 is_a: EDAM:0000947 ! Biological pathway map
 relationship: is_attribute_of EDAM:0000008 ! Undefined
@@ -23638,7 +24565,7 @@ relationship: has_identifier EDAM:0001082 ! Biological pathway identifier
 id: EDAM:0001657
 name: Genetic information processing pathway map
 namespace: data
-def: "A map (typically a diagram) of a genetic information processing pathway." [EDAM:EBI "EMBRACE definition"]
+def: "A report including a map (typically a diagram) of a genetic information processing pathway." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000947 ! Biological pathway map
 relationship: is_attribute_of EDAM:0000008 ! Undefined
 relationship: is_input_of EDAM:0000223 ! Undefined
@@ -23652,7 +24579,7 @@ relationship: has_identifier EDAM:0001082 ! Biological pathway identifier
 id: EDAM:0001658
 name: Environmental information processing pathway map
 namespace: data
-def: "A map (typically a diagram) of an environmental information processing pathway." [EDAM:EBI "EMBRACE definition"]
+def: "A report including a map (typically a diagram) of an environmental information processing pathway." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000947 ! Biological pathway map
 relationship: is_attribute_of EDAM:0000008 ! Undefined
 relationship: is_input_of EDAM:0000223 ! Undefined
@@ -23665,7 +24592,7 @@ relationship: has_identifier EDAM:0001082 ! Biological pathway identifier
 id: EDAM:0001659
 name: Signal transduction pathway map
 namespace: data
-def: "A map (typically a diagram) of a signal transduction pathway." [EDAM:EBI "EMBRACE definition"]
+def: "A report including a map (typically a diagram) of a signal transduction pathway." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000947 ! Biological pathway map
 relationship: is_attribute_of EDAM:0000008 ! Undefined
 relationship: is_input_of EDAM:0000223 ! Undefined
@@ -23678,7 +24605,7 @@ relationship: has_identifier EDAM:0001082 ! Biological pathway identifier
 id: EDAM:0001660
 name: Cellular process pathway map
 namespace: data
-def: "A map (typically a diagram) of a cellular process pathway." [EDAM:EBI "EMBRACE definition"]
+def: "A report including a map (typically a diagram) of a cellular process pathway." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000947 ! Biological pathway map
 relationship: is_attribute_of EDAM:0000008 ! Undefined
 relationship: is_input_of EDAM:0000223 ! Undefined
@@ -23690,7 +24617,7 @@ relationship: has_identifier EDAM:0001082 ! Biological pathway identifier
 id: EDAM:0001661
 name: Disease pathway map
 namespace: data
-def: "A map of a disease pathway, typically a diagram for a human disease." [EDAM:EBI "EMBRACE definition"]
+def: "A report including a map of a disease pathway, typically a diagram for a human disease." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000947 ! Biological pathway map
 relationship: is_attribute_of EDAM:0000008 ! Undefined
 relationship: is_input_of EDAM:0000223 ! Undefined
@@ -23702,7 +24629,7 @@ relationship: has_identifier EDAM:0001082 ! Biological pathway identifier
 id: EDAM:0001662
 name: Drug structure map
 namespace: data
-def: "A map (typically a diagram) of drug structure relationships." [EDAM:EBI "EMBRACE definition"]
+def: "A report including a map (typically a diagram) of drug structure relationships." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000947 ! Biological pathway map
 relationship: is_attribute_of EDAM:0000008 ! Undefined
 relationship: is_input_of EDAM:0000223 ! Undefined
@@ -23715,7 +24642,7 @@ relationship: has_identifier EDAM:0001082 ! Biological pathway identifier
 id: EDAM:0001663
 name: Protein-protein interaction network map
 namespace: data
-def: "A map (typically a diagram) of a network of protein interactions." [EDAM:EBI "EMBRACE definition"]
+def: "A report including a map (typically a diagram) of a network of protein interactions." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0000947 ! Biological pathway map
 relationship: is_attribute_of EDAM:0000008 ! Undefined
 relationship: is_input_of EDAM:0000223 ! Undefined
@@ -24537,7 +25464,7 @@ id: EDAM:0001773
 name: Tool-specific parameter
 namespace: data
 def: "Some simple value(s) controlling an operation specific to a single (or few) tools only." [EDAM:EBI "EMBRACE definition"]
-comment: This term should be used in preference to introducing many tool-specific terms into the ontology.  It should never have child terms.
+comment: This term should be used in preference to introducing many tool-specific terms into the ontology. It should never have child terms.
 is_a: EDAM:0002029 ! Parameter
 relationship: is_attribute_of EDAM:0000008 ! Undefined
 relationship: is_input_of EDAM:0000223 ! Undefined
@@ -24702,7 +25629,7 @@ relationship: has_source EDAM:0000580 ! Undefined
 id: EDAM:0002151
 name: Colour
 namespace: data
-def: "Specification of one or or more colours." [EDAM:EBI "EMBRACE definition"]
+def: "Specification of one or more colours." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002152 ! Rendering parameter
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
@@ -24801,7 +25728,7 @@ id: EDAM:0000852
 name: Sequence mask type
 namespace: data
 def: "The type of sequence masking to perform." [EDAM:EBI "EMBRACE definition"]
-comment: Sequence masking is where specific characters or positions in a molecular sequence are masked (replaced) with an another (mask character).  The mask type indicates what is masked, for example regions that are not of interest or which are information-poor including acidic protein regions, basic protein regions, proline-rich regions, low compositional complexity regions, short-periodicity internal repeats, simple repeats and low complexity regions.  Masked sequences are used in database search to eliminate statistically significant but biologically uninteresting hits.
+comment: Sequence masking is where specific characters or positions in a molecular sequence are masked (replaced) with an another (mask character). The mask type indicates what is masked, for example regions that are not of interest or which are information-poor including acidic protein regions, basic protein regions, proline-rich regions, low compositional complexity regions, short-periodicity internal repeats, simple repeats and low complexity regions. Masked sequences are used in database search to eliminate statistically significant but biologically uninteresting hits.
 is_a: EDAM:0002023 ! Sequence mask data
 relationship: is_attribute_of EDAM:0000008 ! Undefined
 relationship: is_input_of EDAM:0000223 ! Undefined
@@ -24871,7 +25798,7 @@ relationship: has_identifier EDAM:0000841 ! Undefined
 id: EDAM:0002012
 name: Map position
 namespace: data
-def: "A position in a map (for example a genetic map), either a single position (point) or a region / interval.  This includes position in genomes based on a reference sequence." [EDAM:EBI "EMBRACE definition"]
+def: "A position in a map (for example a genetic map), either a single position (point) or a region / interval. This includes position in genomes based on a reference sequence." [EDAM:EBI "EMBRACE definition"]
 comment: A position may be specified for any mappable object, i.e. anything that may have positional information such as a physical position in a chromosome.
 xref: Moby:GCP_MapPoint
 xref: Moby:GCP_MapPosition
@@ -24960,7 +25887,7 @@ relationship: is_attribute_of EDAM:0000010 ! Entity feature
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
-relationship: has_identifier EDAM:0001893 ! Locus identifier
+relationship: has_identifier EDAM:0001893 ! Locus ID
 
 !
 ! Data<-Parameter<-Sequence position specification<-Map position<-Locus
@@ -24978,7 +25905,7 @@ relationship: is_attribute_of EDAM:0000010 ! Entity feature
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 relationship: has_source EDAM:0000580 ! Undefined
-relationship: has_identifier EDAM:0001893 ! Locus identifier
+relationship: has_identifier EDAM:0001893 ! Locus ID
 
 
 
@@ -25488,10 +26415,10 @@ relationship: has_identifier EDAM:0000841 ! Undefined
 !
 [Term]
 id: EDAM:0001696
-name: Drug
+name: Drug annotation
 namespace: data
 def: "An informative report on a specific drug." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0000962 ! Chemical compound
+is_a: EDAM:0000962 ! Chemical compound annotation
 relationship: is_attribute_of EDAM:0000008 ! Undefined
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
@@ -25515,7 +26442,7 @@ relationship: has_identifier EDAM:0001086 ! Chemical compound identifier
 
 
 !
-! Data<-Chemical compound<-Drug
+! Data<-Chemical compound<-Drug annotation
 !
 
 
@@ -25523,7 +26450,7 @@ relationship: has_identifier EDAM:0001086 ! Chemical compound identifier
 
 
 !
-! Data<-Organism strain data
+! Data<-Cell line
 !
 
 
@@ -25698,6 +26625,23 @@ relationship: has_source EDAM:0000580 ! Undefined
 relationship: has_identifier EDAM:0000841 ! Undefined
 
 
+
+!
+! Data<-Virus report
+!
+[Term]
+id: EDAM:0002308
+name: Virus taxonomy report
+namespace: data
+def: "An informative report on the taxonomy of a specific virus." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0002307 ! Virus report
+relationship: is_attribute_of EDAM:0000008 ! Undefined
+relationship: is_input_of EDAM:0000223 ! Undefined
+relationship: is_output_of EDAM:0000223 ! Undefined
+relationship: has_source EDAM:0000580 ! Undefined
+relationship: has_identifier EDAM:0000841 ! Undefined
+
+
 !
 ! Data<-Ontology term
 !
@@ -25729,7 +26673,7 @@ relationship: is_attribute_of EDAM:0000008 ! Undefined
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 ! relationship: has_source EDAM:0000830 ! Gene Ontology
-relationship: has_identifier EDAM:0001176 ! GO term identifier
+relationship: has_identifier EDAM:0001176 ! GO term ID
 
 [Term]
 id: EDAM:0001717
@@ -25869,7 +26813,7 @@ relationship: is_attribute_of EDAM:0000008 ! Undefined
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 ! relationship: has_source EDAM:0000830 ! Gene Ontology
-relationship: has_identifier EDAM:0001176 ! GO term identifier
+relationship: has_identifier EDAM:0001176 ! GO term ID
 
 [Term]
 id: EDAM:0001728
@@ -25882,7 +26826,7 @@ relationship: is_attribute_of EDAM:0000008 ! Undefined
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 ! relationship: has_source EDAM:0000830 ! Gene Ontology
-relationship: has_identifier EDAM:0001176 ! GO term identifier
+relationship: has_identifier EDAM:0001176 ! GO term ID
 
 [Term]
 id: EDAM:0001729
@@ -25895,7 +26839,7 @@ relationship: is_attribute_of EDAM:0000008 ! Undefined
 relationship: is_input_of EDAM:0000223 ! Undefined
 relationship: is_output_of EDAM:0000223 ! Undefined
 ! relationship: has_source EDAM:0000830 ! Gene Ontology
-relationship: has_identifier EDAM:0001176 ! GO term identifier
+relationship: has_identifier EDAM:0001176 ! GO term ID
 
 
 
@@ -26145,7 +27089,6 @@ namespace: format
 def: "Data format for a biological pathway." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0001915 ! Data format
 
-
 [Term]
 id: EDAM:0002014
 name: Sequence-profile alignment format
@@ -26184,7 +27127,7 @@ is_a: EDAM:0001915 ! Data format
 
 [Term]
 id: EDAM:0002030
-name: Chemical compound report format
+name: Chemical compound annotation format
 namespace: format
 def: "Format of a report on a chemical compound." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0001915 ! Data format
@@ -26203,7 +27146,6 @@ namespace: format
 def: "Format of a workflow." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0001915 ! Data format
 
-
 [Term]
 id: EDAM:0002035
 name: Chemical formula format
@@ -26425,7 +27367,7 @@ is_a: EDAM:0001915 ! Data format
 id: EDAM:0002210
 name: Strain data format
 namespace: format
-def: "Format of a report on organism strain data." [EDAM:EBI "EMBRACE definition"]
+def: "Format of a report on organism strain data / cell line." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0001915 ! Data format
 
 
@@ -26698,16 +27640,18 @@ is_a: EDAM:0001919 ! Sequence record format
 
 [Term]
 id: EDAM:0001967
-name: das sequence format
+name: das
 namespace: format
-def: "DASSEQUENCE DAS sequence format (any type)." [EDAM:EBI "EMBRACE definition"]
+def: "DAS sequence (XML) format (any type)." [EDAM:EBI "EMBRACE definition"]
+synonym: "das sequence format" EXACT []
 is_a: EDAM:0001919 ! Sequence record format
 
 [Term]
 id: EDAM:0001968
 name: dasdna sequence format
 namespace: format
-def: "DASDNA DAS sequence format (nucleotide-only)." [EDAM:EBI "EMBRACE definition"]
+def: "DAS sequence (XML) format (nucleotide-only)." [EDAM:EBI "EMBRACE definition"]
+comment: The use of this format is deprecated.
 is_a: EDAM:0001919 ! Sequence record format
 
 [Term]
@@ -26776,7 +27720,7 @@ id: EDAM:0002204
 name: embl xml sequence format
 namespace: format
 def: "An XML format for EMBL entries." [EDAM:EBI "EMBRACE definition"]
-comment: This is a placeholder for other more specific terms.  It should not normally be used for annotation.
+comment: This is a placeholder for other more specific terms. It should not normally be used for annotation.
 is_a: EDAM:0002202 ! Sequence record full format
 ! relationship: has_identifier EDAM:0001103 ! EMBL/GenBank/DDBJ accession number
 
@@ -26810,13 +27754,27 @@ is_a: EDAM:0002202 ! Sequence record full format
 !
 [Term]
 id: EDAM:0001927
-name: embl sequence format
+name: embl
 namespace: format
 def: "EMBL entry format." [EDAM:EBI "EMBRACE definition"]
+synonym: "embl sequence format" EXACT []
+synonym: "EMBL" EXACT []
+is_a: EDAM:0002181 ! embl-like sequence format
+! relationship: has_identifier EDAM:0001103 ! EMBL/GenBank/DDBJ accession number
+
+[Term]
+id: EDAM:0002311
+name: embl-html
+namespace: format
+def: "EMBL entry format wrapped in HTML elements." [EDAM:EBI "EMBRACE definition"]
+synonym: "embl sequence format" EXACT []
+synonym: "EMBL" EXACT []
 is_a: EDAM:0002181 ! embl-like sequence format
 ! relationship: has_identifier EDAM:0001103 ! EMBL/GenBank/DDBJ accession number
 
 
+
+
 [Term]
 id: EDAM:0002186
 name: geneseq sequence format
@@ -26869,6 +27827,18 @@ is_a: EDAM:0002205 ! genbank-like sequence format
 ! relationship: has_identifier EDAM:0001103 ! EMBL/GenBank/DDBJ accession number
 
 [Term]
+id: EDAM:0002313
+name: genbank-html
+namespace: format
+def: "Genbank entry format wrapped in HTML elements." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0002205 ! genbank-like sequence format
+! relationship: has_identifier EDAM:0001103 ! EMBL/GenBank/DDBJ accession number
+
+
+
+
+
+[Term]
 id: EDAM:0001937
 name: genpept sequence format
 namespace: format
@@ -26963,9 +27933,18 @@ is_a: EDAM:0002182 ! fastq-like sequence format
 !
 [Term]
 id: EDAM:0001929
-name: fasta sequence format
+name: fasta
 namespace: format
 def: "FASTA format including NCBI-style IDs." [EDAM:EBI "EMBRACE definition"]
+synonym: "FASTA" EXACT []
+synonym: "fasta sequence format" EXACT []
+is_a: EDAM:0002200 ! fasta-like sequence format
+
+[Term]
+id: EDAM:0002310
+name: fasta-html
+namespace: format
+def: "FASTA format wrapped in HTML elements." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002200 ! fasta-like sequence format
 
 [Term]
@@ -27045,14 +28024,16 @@ is_a: EDAM:0001920 ! Sequence feature annotation format
 
 [Term]
 id: EDAM:0001978
-name: dasgff feature format
+name: dasgff
 namespace: format
-def: "DAS GFF feature format." [EDAM:EBI "EMBRACE definition"]
+def: "DAS GFF (XML) feature format." [EDAM:EBI "EMBRACE definition"]
+synonym: "dasgff feature" EXACT []
+synonym: "das feature" EXACT []
 is_a: EDAM:0001920 ! Sequence feature annotation format
 
 [Term]
 id: EDAM:0001979
-name: debug feature format
+name: debug feature
 namespace: format
 def: "EMBOSS debugging trace feature format of full internal data content." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0001920 ! Sequence feature annotation format
@@ -27063,49 +28044,71 @@ is_a: EDAM:0001920 ! Sequence feature annotation format
 !
 ! Data format<-Sequence feature annotation format<-Sequence feature table format
 !
-[Term]
-id: EDAM:0001974
-name: gff2 feature format
-namespace: format
-def: "GFF version 1 or 2 feature format." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0001920 ! Sequence feature annotation format
 
 [Term]
-id: EDAM:0001975
-name: gff3 feature format
+id: EDAM:0002305
+name: gff feature
 namespace: format
-def: "GFF version 3 feature format." [EDAM:EBI "EMBRACE definition"]
+def: "GFF feature format (of indeterminate version)." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0001920 ! Sequence feature annotation format
 
+
 [Term]
 id: EDAM:0001976
-name: pir feature format
+name: pir feature
 namespace: format
 def: "PIR feature format." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0001920 ! Sequence feature annotation format
 
 [Term]
 id: EDAM:0001977
-name: swiss feature format
+name: swiss feature
 namespace: format
 def: "SwissProt feature format." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0001920 ! Sequence feature annotation format
 
 [Term]
 id: EDAM:0001980
-name: embl feature format
+name: embl feature
 namespace: format
 def: "EMBL feature format." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0001920 ! Sequence feature annotation format
 
 [Term]
 id: EDAM:0001981
-name: genbank feature format
+name: genbank feature
 namespace: format
 def: "Genbank feature format." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0001920 ! Sequence feature annotation format
 
 
+
+!
+! Data format<-Sequence feature annotation format<-Sequence feature table format<-gff feature
+!
+[Term]
+id: EDAM:0001974
+name: gff2 feature
+namespace: format
+def: "GFF version 1 or 2 feature format." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0002305 ! gff feature
+
+[Term]
+id: EDAM:0001975
+name: gff3 feature
+namespace: format
+def: "GFF version 3 feature format." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0002305 ! gff feature
+
+[Term]
+id: EDAM:0002306
+name: gtf feature
+namespace: format
+def: "GFF feature format with extra tags." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0002305 ! gff feature
+
+
+
 !
 ! Data format<-Alignment format
 !
@@ -27282,7 +28285,7 @@ is_a: EDAM:0001921 ! Alignment format
 id: EDAM:0001391
 name: HMMER sequence alignment format
 namespace: format
-def: "Multiple sequences aligned by HMMER package to an HMM, in FASTA-style format." [EDAM:EBI "EMBRACE definition"]
+def: "FASTA-style format for multiple sequences aligned by HMMER package to an HMM." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0001921 ! Alignment format
 
 
@@ -27390,9 +28393,10 @@ is_a: EDAM:0002033 ! Tertiary structure format
 !
 [Term]
 id: EDAM:0001476
-name: PDB file format
+name: pdb
 namespace: format
-def: "An entry from the PDB database in PDB format, or any report in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "Entry format of PDB database in PDB format, or any report in the same format." [EDAM:EBI "EMBRACE definition"]
+synonym: "PDB" EXACT []
 xref: Moby:PDB-formatted-text
 xref: Moby:PDB-Text
 is_a: EDAM:0001475 ! PDB database entry format
@@ -27401,9 +28405,10 @@ is_a: EDAM:0001475 ! PDB database entry format
 
 [Term]
 id: EDAM:0001477
-name: mmCIF file format
+name: mmCIF
 namespace: format
-def: "An entry from the PDB database in mmCIF format, or any report in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "Entry format of PDB database in mmCIF format, or any report in the same format." [EDAM:EBI "EMBRACE definition"]
+synonym: "mmcif" EXACT []
 xref: Moby:mmCIF-Text
 xref: Moby:mmCIF_Text
 is_a: EDAM:0001475 ! PDB database entry format
@@ -27412,9 +28417,10 @@ is_a: EDAM:0001475 ! PDB database entry format
 
 [Term]
 id: EDAM:0001478
-name: PDBML file format
+name: pdbml
 namespace: format
-def: "An entry from the PDB database in PDBML (XML) format, or any report in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "Entry format of PDB database in PDBML (XML) format, or any report in the same format." [EDAM:EBI "EMBRACE definition"]
+synonym: "PDBML" EXACT []
 is_a: EDAM:0001475 ! PDB database entry format
 ! relationship: has_source EDAM:0000701 ! PDB database
 ! relationship: has_identifier EDAM:0001127 ! PDB identifier
@@ -27599,7 +28605,7 @@ is_a: EDAM:0002017 ! Amino acid index format
 id: EDAM:0001739
 name: PubMed Central article format
 namespace: format
-def: "An article from the PubMed Central database." [EDAM:EBI "EMBRACE definition"]
+def: "Article format of the PubMed Central database." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002020 ! Article format
 ! relationship: has_source EDAM:0000776 ! PubMed Central database
 ! relationship: has_identifier EDAM:0001187 ! PubMed unique identifier
@@ -27620,7 +28626,7 @@ is_a: EDAM:0002020 ! Article format
 id: EDAM:0001740
 name: iHOP text mining abstract format
 namespace: format
-def: "An iHOP abstract." [EDAM:EBI "EMBRACE definition"]
+def: "iHOP abstract format." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002021 ! Text mining report format
 
 
@@ -27628,7 +28634,7 @@ is_a: EDAM:0002021 ! Text mining report format
 id: EDAM:0001741
 name: Oscar3 text mining abstract format
 namespace: format
-def: "Text mining abstract from the Oscar 3 application." [EDAM:EBI "EMBRACE definition"]
+def: "Text mining abstract format from the Oscar 3 application." [EDAM:EBI "EMBRACE definition"]
 comment: Oscar 3 performs chemistry-specific parsing of chemical documents. It attempts to identify chemical names, ontology terms and chemical data from a document.
 is_a: EDAM:0002021 ! Text mining report format
 
@@ -27641,21 +28647,21 @@ is_a: EDAM:0002021 ! Text mining report format
 id: EDAM:0001582
 name: EMBOSS findkm enzyme kinetics report format
 namespace: format
-def: "A report format for the kinetics of enzyme-catalysed reaction(s) in a format generated by EMBOSS findkm.  This includes Michaelis Menten plot, Hanes Woolf plot, Michaelis Menten constant (Km) and maximum velocity (Vmax)." [EDAM:EBI "EMBRACE definition"]
+def: "A report format for the kinetics of enzyme-catalysed reaction(s) in a format generated by EMBOSS findkm. This includes Michaelis Menten plot, Hanes Woolf plot, Michaelis Menten constant (Km) and maximum velocity (Vmax)." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002027 ! Enzyme kinetics report format
 
 
 
 
 !
-! Data format<-Chemical compound report format
+! Data format<-Chemical compound annotation format
 !
 [Term]
 id: EDAM:0001697
 name: KEGG LIGAND entry format
 namespace: format
 def: "The format of an entry from the KEGG LIGAND chemical database." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0002030 ! Chemical compound report format
+is_a: EDAM:0002030 ! Chemical compound annotation format
 ! relationship: has_source EDAM:0000706 ! KEGG LIGAND database
 ! relationship: has_identifier EDAM:0001154 ! KEGG object identifier
 
@@ -27665,7 +28671,7 @@ id: EDAM:0001698
 name: KEGG COMPOUND entry format
 namespace: format
 def: "The format of an entry from the KEGG COMPOUND database." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0002030 ! Chemical compound report format
+is_a: EDAM:0002030 ! Chemical compound annotation format
 ! relationship: has_source EDAM:0000707 ! KEGG COMPOUND database
 ! relationship: has_identifier EDAM:0001154 ! KEGG object identifier
 
@@ -27675,7 +28681,7 @@ id: EDAM:0001699
 name: KEGG PLANT entry format
 namespace: format
 def: "The format of an entry from the KEGG PLANT database." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0002030 ! Chemical compound report format
+is_a: EDAM:0002030 ! Chemical compound annotation format
 ! relationship: has_source EDAM:0000708 ! KEGG PLANT database
 ! relationship: has_identifier EDAM:0001154 ! KEGG object identifier
 
@@ -27685,7 +28691,7 @@ id: EDAM:0001700
 name: KEGG GLYCAN entry format
 namespace: format
 def: "The format of an entry from the KEGG GLYCAN database." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0002030 ! Chemical compound report format
+is_a: EDAM:0002030 ! Chemical compound annotation format
 ! relationship: has_source EDAM:0000710 ! KEGG GLYCAN database
 ! relationship: has_identifier EDAM:0001154 ! KEGG object identifier
 
@@ -27694,7 +28700,7 @@ id: EDAM:0001706
 name: KEGG DRUG entry format
 namespace: format
 def: "The format of an entry from the KEGG DRUG database." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0002030 ! Chemical compound report format
+is_a: EDAM:0002030 ! Chemical compound annotation format
 ! relationship: has_source EDAM:0000709 ! KEGG DRUG database
 ! relationship: has_identifier EDAM:0001154 ! KEGG object identifier
 
@@ -27703,7 +28709,7 @@ id: EDAM:0001701
 name: PubChem entry format
 namespace: format
 def: "The format of an entry from PubChem." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0002030 ! Chemical compound report format
+is_a: EDAM:0002030 ! Chemical compound annotation format
 ! relationship: has_source EDAM:0000712 ! PubChem database
 ! relationship: has_identifier EDAM:0001172 ! PubChem Compound accession identifier (CID)
 
@@ -27713,7 +28719,7 @@ id: EDAM:0001702
 name: ChemSpider entry format
 namespace: format
 def: "The format of an entry from a database of chemical structures and property predictions." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0002030 ! Chemical compound report format
+is_a: EDAM:0002030 ! Chemical compound annotation format
 ! relationship: has_source EDAM:0000713 ! ChemSpider database
 ! relationship: has_identifier EDAM:0001173 ! ChemSpider ID
 
@@ -27724,7 +28730,7 @@ name: ChEBI entry format
 namespace: format
 def: "The format of an entry from Chemical Entities of Biological Interest (ChEBI)." [EDAM:EBI "EMBRACE definition"]
 comment: ChEBI includes an ontological classification defining relations between entities or classes of entities.
-is_a: EDAM:0002030 ! Chemical compound report format
+is_a: EDAM:0002030 ! Chemical compound annotation format
 ! relationship: has_source EDAM:0000714 ! ChEBI database
 ! relationship: has_identifier EDAM:0001174 ! ChEBI identifier
 
@@ -27734,7 +28740,7 @@ id: EDAM:0001704
 name: MSDchem ligand dictionary entry format
 namespace: format
 def: "The format of an entry from the MSDchem ligand dictionary." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0002030 ! Chemical compound report format
+is_a: EDAM:0002030 ! Chemical compound annotation format
 ! relationship: has_source EDAM:0000715 ! MSDchem ligand dictionary database
 ! relationship: has_identifier EDAM:0000992 ! Ligand identifier
 
@@ -27744,7 +28750,7 @@ id: EDAM:0001705
 name: HET group dictionary entry format
 namespace: format
 def: "The format of an entry from the HET group dictionary (HET groups from PDB files)." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0002030 ! Chemical compound report format
+is_a: EDAM:0002030 ! Chemical compound annotation format
 ! relationship: has_source EDAM:0000716 ! HET group dictionary
 ! relationship: has_identifier EDAM:0000992 ! Ligand identifier
 
@@ -27756,8 +28762,8 @@ is_a: EDAM:0002030 ! Chemical compound report format
 id: EDAM:0001808
 name: GeneIlluminator gene report format
 namespace: format
-def: "A report on biological functions associated with a gene symbol and its alternative names (synomyms, homonyms), as generated by the GeneIlluminater service, or any file in the same format." [EDAM:EBI "EMBRACE definition"]
-comment: This includes a gene name and gene symbol (abbreviation of the name) which may be in a namespace indicating the gene status and relevant organisation.
+def: "Report format for biological functions associated with a gene name and its alternative names (synomyms, homonyms), as generated by the GeneIlluminater service." [EDAM:EBI "EMBRACE definition"]
+comment: This includes a gene name and abbreviation of the name which may be in a namespace indicating the gene status and relevant organisation.
 xref: Moby:GI_Gene
 is_a: EDAM:0002031 ! Gene annotation format
 ! relationship: has_source EDAM:0000007 ! Tool
@@ -27766,7 +28772,7 @@ is_a: EDAM:0002031 ! Gene annotation format
 id: EDAM:0001809
 name: BacMap gene card format
 namespace: format
-def: "An informative report on the DNA and protein sequences for a given gene label from a bacterial chromosome maps from the BacMap database." [EDAM:EBI "EMBRACE definition"]
+def: "Format of a report on the DNA and protein sequences for a given gene label from a bacterial chromosome maps from the BacMap database." [EDAM:EBI "EMBRACE definition"]
 xref: Moby:BacMapGeneCard
 is_a: EDAM:0002031 ! Gene annotation format
 ! relationship: has_source EDAM:0002011 ! BacMap database
@@ -27775,18 +28781,34 @@ is_a: EDAM:0002031 ! Gene annotation format
 id: EDAM:0001810
 name: ColiCard report format
 namespace: format
-def: "A detailed report on Escherichia coli genes, proteins and molecules from the CyberCell Database (CCDB)." [EDAM:EBI "EMBRACE definition"]
+def: "Format of a report on Escherichia coli genes, proteins and molecules from the CyberCell Database (CCDB)." [EDAM:EBI "EMBRACE definition"]
 xref: Moby:ColiCard
 is_a: EDAM:0002031 ! Gene annotation format
 ! relationship: has_source EDAM:0000670 ! CCDB database
 
+[Term]
+id: EDAM:0002328
+name: PseudoCAP gene report format
+namespace: format
+def: "Format of a report on a gene from the PseudoCAP database." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0002031 ! Gene annotation format
+! relationship: has_source EDAM:0000670 ! CCDB database
+
+[Term]
+id: EDAM:0002329
+name: GeneCards gene report format
+namespace: format
+def: "Format of a report on a gene from the GeneCards database." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0002031 ! Gene annotation format
+! relationship: has_source EDAM:0000670 ! CCDB database
+
 
 
 [Term]
 id: EDAM:0001603
 name: Ensembl gene report format
 namespace: format
-def: "An entry from the Ensembl genome database or any file in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "Entry format of Ensembl genome database." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002031 ! Gene annotation format
 ! relationship: has_source EDAM:0000680 ! Ensembl database
 ! relationship: has_identifier EDAM:0001033 ! Ensembl identifier
@@ -27795,7 +28817,7 @@ is_a: EDAM:0002031 ! Gene annotation format
 id: EDAM:0001604
 name: DictyBase gene report format
 namespace: format
-def: "An entry from the DictyBase genome database or any file in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "Entry format of DictyBase genome database." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002031 ! Gene annotation format
 ! relationship: has_source EDAM:0000681 ! DictyBase database
 ! relationship: has_identifier EDAM:0001032 ! DictyBase ID
@@ -27804,7 +28826,7 @@ is_a: EDAM:0002031 ! Gene annotation format
 id: EDAM:0001605
 name: CGD gene report format
 namespace: format
-def: "An entry from the Candida Genome database or any file in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "Entry format of Candida Genome database." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002031 ! Gene annotation format
 ! relationship: has_source EDAM:0000683 ! CGD database
 ! relationship: has_identifier EDAM:0001031 ! CGD ID
@@ -27814,7 +28836,7 @@ is_a: EDAM:0002031 ! Gene annotation format
 id: EDAM:0001606
 name: DragonDB gene report format
 namespace: format
-def: "An entry from the DragonDB genome database or any file in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "Entry format of DragonDB genome database." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002031 ! Gene annotation format
 ! relationship: has_source EDAM:0000672 ! DragonDB database
 
@@ -27822,7 +28844,7 @@ is_a: EDAM:0002031 ! Gene annotation format
 id: EDAM:0001607
 name: EcoCyc gene report format
 namespace: format
-def: "An entry from the EcoCyc genome database or any file in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "Entry format of EcoCyc genome database." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002031 ! Gene annotation format
 ! relationship: has_source EDAM:0000673 ! EcoCyc database
 
@@ -27832,7 +28854,7 @@ is_a: EDAM:0002031 ! Gene annotation format
 id: EDAM:0001608
 name: FlyBase gene report format
 namespace: format
-def: "An entry from the FlyBase genome database or any file in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "Entry format of FlyBase genome database." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002031 ! Gene annotation format
 ! relationship: has_source EDAM:0000685 ! FlyBase database
 ! relationship: has_identifier EDAM:0001089 ! FlyBase identifier
@@ -27842,7 +28864,7 @@ is_a: EDAM:0002031 ! Gene annotation format
 id: EDAM:0001609
 name: Gramene gene report format
 namespace: format
-def: "An entry from the Gramene genome database or any file in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "Entry format of Gramene genome database." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002031 ! Gene annotation format
 ! relationship: has_source EDAM:0000808 ! Gramene database
 ! relationship: has_identifier EDAM:0001102 ! Gramene primary identifier
@@ -27852,16 +28874,16 @@ is_a: EDAM:0002031 ! Gene annotation format
 id: EDAM:0001610
 name: KEGG GENES gene report format
 namespace: format
-def: "An entry from the KEGG GENES genome database or any file in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "Entry format of KEGG GENES genome database." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002031 ! Gene annotation format
 ! relationship: has_source EDAM:0000802 ! KEGG GENES database
-! relationship: has_identifier EDAM:0002103 ! KEGG GENES entry name
+! relationship: has_identifier EDAM:0002103 ! Gene name (KEGG GENES)
 
 [Term]
 id: EDAM:0001611
 name: MaizeGDB gene report format
 namespace: format
-def: "An entry from the Maize genetics and genomics database (MaizeGDB) or any file in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "Entry format of the Maize genetics and genomics database (MaizeGDB)." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002031 ! Gene annotation format
 ! relationship: has_source EDAM:0000788 ! MaizeGDB database
 
@@ -27870,7 +28892,7 @@ is_a: EDAM:0002031 ! Gene annotation format
 id: EDAM:0001612
 name: MGD gene report format
 namespace: format
-def: "An entry from the Mouse Genome Database (MGD) or any file in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "Entry format of the Mouse Genome Database (MGD)." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002031 ! Gene annotation format
 ! relationship: has_source EDAM:0000688 ! MGD database
 
@@ -27880,7 +28902,7 @@ is_a: EDAM:0002031 ! Gene annotation format
 id: EDAM:0001613
 name: RGD gene report format
 namespace: format
-def: "An entry from the Rat Genome Database (RGD) or any file in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "Entry format of the Rat Genome Database (RGD)." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002031 ! Gene annotation format
 ! relationship: has_source EDAM:0000689 ! RGD database
 
@@ -27890,7 +28912,7 @@ is_a: EDAM:0002031 ! Gene annotation format
 id: EDAM:0001614
 name: SGD gene report format
 namespace: format
-def: "An entry from the Saccharomyces Genome Database (SGD) or any file in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "Entry format of the Saccharomyces Genome Database (SGD)." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002031 ! Gene annotation format
 ! relationship: has_source EDAM:0000684 ! SGD database
 ! relationship: has_identifier EDAM:0001034 ! SGD identifier
@@ -27900,10 +28922,10 @@ is_a: EDAM:0002031 ! Gene annotation format
 id: EDAM:0001615
 name: GeneDB gene report format
 namespace: format
-def: "An entry from the Sanger GeneDB genome database or any file in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "Entry format of the Sanger GeneDB genome database." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002031 ! Gene annotation format
 ! relationship: has_source EDAM:0000674 ! GeneDB database
-! relationship: has_identifier EDAM:0001035 ! GeneDB identifier
+! relationship: has_identifier EDAM:0001035 ! Gene ID (GeneDB)
 
 
 
@@ -27912,7 +28934,7 @@ is_a: EDAM:0002031 ! Gene annotation format
 id: EDAM:0001616
 name: TAIR gene report format
 namespace: format
-def: "An entry from The Arabidopsis Information Resource (TAIR) genome database or any file in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "Entry format of The Arabidopsis Information Resource (TAIR) genome database." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002031 ! Gene annotation format
 ! relationship: has_source EDAM:0000789 ! TAIR database
 ! relationship: has_identifier EDAM:0001037 ! TAIR identifier
@@ -27922,7 +28944,7 @@ is_a: EDAM:0002031 ! Gene annotation format
 id: EDAM:0001617
 name: WormBase gene report format
 namespace: format
-def: "An entry from the WormBase genomes database or any file in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "Entry format of the WormBase genomes database." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002031 ! Gene annotation format
 ! relationship: has_source EDAM:0000686 ! WormBase database
 ! relationship: has_identifier EDAM:0001091 ! WormBase name
@@ -27934,7 +28956,7 @@ is_a: EDAM:0002031 ! Gene annotation format
 id: EDAM:0001618
 name: ZFIN gene report format
 namespace: format
-def: "An entry from the Zebrafish Information Network (ZFIN) genome database or any file in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "Entry format of the Zebrafish Information Network (ZFIN) genome database." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002031 ! Gene annotation format
 ! relationship: has_source EDAM:0000690 ! ZFIN database
 
@@ -27943,7 +28965,7 @@ is_a: EDAM:0002031 ! Gene annotation format
 id: EDAM:0001619
 name: TIGR gene report format
 namespace: format
-def: "An entry from the TIGR genome database or any file in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "Entry format of the TIGR genome database." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002031 ! Gene annotation format
 ! relationship: has_source EDAM:0000799 ! TIGR database
 ! relationship: has_identifier EDAM:0001036 ! TIGR identifier
@@ -27952,7 +28974,7 @@ is_a: EDAM:0002031 ! Gene annotation format
 id: EDAM:0001782
 name: NCBI gene report format
 namespace: format
-def: "An entry (gene) from the NCBI database, or any file in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "Entry (gene) format of the NCBI database." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002031 ! Gene annotation format
 ! relationship: has_source EDAM:0000799 ! RefSeq database
 ! relationship: has_identifier EDAM:0001027 ! NCBI gene ID
@@ -28027,7 +29049,7 @@ is_a: EDAM:0002035 ! Chemical formula format
 id: EDAM:0001200
 name: Chemical formula (SMARTS)
 namespace: format
-def: "Chemical structure specified in SMILES ARbitrary Target Specification (SMARTS), which is a subset of the SMILES line notation." [EDAM:EBI "EMBRACE definition"]
+def: "SMILES ARbitrary Target Specification (SMARTS) format for chemical structure specification, which is a subset of the SMILES line notation." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0001196 ! Chemical formula (SMILES) format
 ! relationship: has_source EDAM:0000696 ! Chemical and small molecule data resource
 ! relationship: has_identifier EDAM:0000990 ! Chemical name
@@ -28116,7 +29138,7 @@ is_a: EDAM:0001431 ! Phylogenetic property values format
 id: EDAM:0001433
 name: PHYLIP discrete states format
 namespace: format
-def: "A file of PHYLIP discrete states data." [EDAM:EBI "EMBRACE definition"]
+def: "Format of PHYLIP discrete states data." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002038 ! Phylogenetic discrete states format
 
 
@@ -28127,7 +29149,7 @@ is_a: EDAM:0002038 ! Phylogenetic discrete states format
 id: EDAM:0001434
 name: PHYLIP cliques file format
 namespace: format
-def: "A file of PHYLIP cliques data." [EDAM:EBI "EMBRACE definition"]
+def: "Format of PHYLIP cliques data." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002039 ! Phylogenetic cliques format
 
 
@@ -28169,7 +29191,7 @@ is_a: EDAM:0002049 ! Phylogenetic tree distance data format
 id: EDAM:0001620
 name: dbSNP polymorphism report format
 namespace: format
-def: "A record from dbSNP or any file in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "Entry format for the dbSNP database." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002051 ! Polymorphism report format
 ! relationship: has_source EDAM:0000810 ! dbSNP database
 ! relationship: has_identifier EDAM:0001106 ! dbSNP identifier
@@ -28182,8 +29204,8 @@ is_a: EDAM:0002051 ! Polymorphism report format
 id: EDAM:0001570
 name: InterPro entry format
 namespace: format
-def: "An entry from the InterPro database of protein signatures (sequence classifiers) and classified sequences." [EDAM:EBI "EMBRACE definition"]
-comment: This includes signature metadata, sequence references and a reference to the signature itself.  There is normally a header (entry accession numbers and name), abstract, taxonomy information, example proteins etc. Each entry also includes a match list which give a number of different views of the signature matches for the sequences in each InterPro entry.
+def: "Entry format for the InterPro database of protein signatures (sequence classifiers) and classified sequences." [EDAM:EBI "EMBRACE definition"]
+comment: This includes signature metadata, sequence references and a reference to the signature itself. There is normally a header (entry accession numbers and name), abstract, taxonomy information, example proteins etc. Each entry also includes a match list which give a number of different views of the signature matches for the sequences in each InterPro entry.
 is_a: EDAM:0002052 ! Protein family report format
 ! relationship: has_source EDAM:0000727 ! InterPro database
 ! relationship: has_identifier EDAM:0001133 ! InterPro primary accession number
@@ -28196,7 +29218,7 @@ is_a: EDAM:0002052 ! Protein family report format
 id: EDAM:0001571
 name: InterPro entry abstract format
 namespace: format
-def: "A textual abstract of signatures in an InterPro entry and its protein matches." [EDAM:EBI "EMBRACE definition"]
+def: "Entry format for the textual abstract of signatures in an InterPro entry and its protein matches." [EDAM:EBI "EMBRACE definition"]
 comment: References are included and a functional inference is made where possible.
 is_a: EDAM:0002052 ! Protein family report format
 ! relationship: has_source EDAM:0000727 ! InterPro database
@@ -28209,7 +29231,7 @@ is_a: EDAM:0002052 ! Protein family report format
 id: EDAM:0001572
 name: Gene3D entry format
 namespace: format
-def: "An entry from the Gene3D protein secondary database or any file in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "Entry format for the Gene3D protein secondary database." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002052 ! Protein family report format
 ! relationship: has_source EDAM:0000728 ! Gene3D database
 ! relationship: has_identifier EDAM:0001135 ! Gene3D ID
@@ -28219,7 +29241,7 @@ is_a: EDAM:0002052 ! Protein family report format
 id: EDAM:0001573
 name: PIRSF entry format
 namespace: format
-def: "An entry from the PIRSF protein secondary database or any file in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "Entry format for the PIRSF protein secondary database." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002052 ! Protein family report format
 ! relationship: has_source EDAM:0000729 ! PIRSF database
 ! relationship: has_identifier EDAM:0001136 ! PIRSF ID
@@ -28230,7 +29252,7 @@ is_a: EDAM:0002052 ! Protein family report format
 id: EDAM:0001574
 name: PRINTS entry format
 namespace: format
-def: "An entry from the PRINTS protein secondary database or any file in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "Entry format for the PRINTS protein secondary database." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002052 ! Protein family report format
 ! relationship: has_source EDAM:0000730 ! PRINTS database
 ! relationship: has_identifier EDAM:0001137 ! PRINTS code
@@ -28242,7 +29264,7 @@ is_a: EDAM:0002052 ! Protein family report format
 id: EDAM:0001575
 name: Panther Families and HMMs entry format
 namespace: format
-def: "An entry from the Panther library of protein families and subfamilies and associated data." [EDAM:EBI "EMBRACE definition"]
+def: "Entry format for the Panther library of protein families and subfamilies." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002052 ! Protein family report format
 ! relationship: has_source EDAM:0000731 ! Panther Families and HMMs database
 
@@ -28253,7 +29275,7 @@ is_a: EDAM:0002052 ! Protein family report format
 id: EDAM:0001576
 name: Pfam entry format
 namespace: format
-def: "An entry from the Pfam protein secondary database or any file in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "Entry format for the Pfam protein secondary database." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002052 ! Protein family report format
 ! relationship: has_source EDAM:0000732 ! Pfam database
 ! relationship: has_identifier EDAM:0001138 ! Pfam accession number
@@ -28263,7 +29285,7 @@ is_a: EDAM:0002052 ! Protein family report format
 id: EDAM:0001577
 name: SMART entry format
 namespace: format
-def: "An entry from the SMART protein secondary database or any file in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "Entry format for the SMART protein secondary database." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002052 ! Protein family report format
 ! relationship: has_source EDAM:0000733 ! SMART database
 ! relationship: has_identifier EDAM:0001139 ! SMART accession number
@@ -28275,7 +29297,7 @@ is_a: EDAM:0002052 ! Protein family report format
 id: EDAM:0001578
 name: Superfamily entry format
 namespace: format
-def: "An entry from the Superfamily protein secondary database or any file in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "Entry format for the Superfamily protein secondary database." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002052 ! Protein family report format
 ! relationship: has_source EDAM:0000734 ! Superfamily Database
 ! relationship: has_identifier EDAM:0001140 ! Superfamily hidden Markov model number
@@ -28285,7 +29307,7 @@ is_a: EDAM:0002052 ! Protein family report format
 id: EDAM:0001579
 name: TIGRFam entry format
 namespace: format
-def: "An entry from the TIGRFam protein secondary database or any file in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "Entry format for the TIGRFam protein secondary database." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002052 ! Protein family report format
 ! relationship: has_source EDAM:0000735 ! TIGRFam database
 ! relationship: has_identifier EDAM:0001141 ! TIGRFam accession number
@@ -28296,7 +29318,7 @@ is_a: EDAM:0002052 ! Protein family report format
 id: EDAM:0001580
 name: ProDom entry format
 namespace: format
-def: "An entry from the ProDom protein domain classification database or any file in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "Entry format for the ProDom protein domain classification database." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002052 ! Protein family report format
 ! relationship: has_source EDAM:0000725 ! ProDom database
 ! relationship: has_identifier EDAM:0001142 ! ProDom accession number
@@ -28306,7 +29328,7 @@ is_a: EDAM:0002052 ! Protein family report format
 id: EDAM:0001581
 name: FSSP entry format
 namespace: format
-def: "An entry from the FSSP database or any file in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "Entry format for the the FSSP database." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002052 ! Protein family report format
 ! relationship: has_source EDAM:0000737 ! FSSP database
 ! relationship: has_identifier EDAM:0001127 ! PDB identifier
@@ -28320,7 +29342,7 @@ is_a: EDAM:0002052 ! Protein family report format
 id: EDAM:0001568
 name: BIND entry format
 namespace: format
-def: "An entry from the BIND database of protein interaction or any file in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "Entry format for the BIND database of protein interaction." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002054 ! Protein interaction format
 ! relationship: has_source EDAM:0000720 ! BIND database
 ! relationship: has_identifier EDAM:0001129 ! BIND accession number
@@ -28330,12 +29352,28 @@ is_a: EDAM:0002054 ! Protein interaction format
 id: EDAM:0001569
 name: IntAct entry format
 namespace: format
-def: "An entry from the IntAct database of protein interaction or any file in the same format." [EDAM:EBI "EMBRACE definition"]
+def: "Entry format for the IntAct database of protein interaction." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002054 ! Protein interaction format
 ! relationship: has_source EDAM:0000721 ! IntAct database
 ! relationship: has_identifier EDAM:0001130 ! IntAct accession number
 
+[Term]
+id: EDAM:0002303
+name: STRING entry format (HTML)
+namespace: format
+def: "Entry format (HTML) for the STRING database of protein interaction." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0002054 ! Protein interaction format
+! relationship: has_source EDAM:0000721 ! IntAct database
+! relationship: has_identifier EDAM:0001130 ! IntAct accession number
 
+[Term]
+id: EDAM:0002304
+name: STRING entry format (XML)
+namespace: format
+def: "Entry format (XML) for the STRING database of protein interaction." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0002054 ! Protein interaction format
+! relationship: has_source EDAM:0000721 ! IntAct database
+! relationship: has_identifier EDAM:0001130 ! IntAct accession number
 
 
 
@@ -28354,7 +29392,7 @@ is_a: EDAM:0002055 ! Sequence assembly format
 id: EDAM:0001631
 name: EXP assembly project file
 namespace: format
-def: "Sequence assembly project file in EXP format." [EDAM:EBI "EMBRACE definition"]
+def: "Sequence assembly project file EXP format." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002055 ! Sequence assembly format
 
 
@@ -28362,7 +29400,7 @@ is_a: EDAM:0002055 ! Sequence assembly format
 id: EDAM:0001632
 name: SCF assembly project file
 namespace: format
-def: "Sequence assembly project file in SCF format." [EDAM:EBI "EMBRACE definition"]
+def: "Sequence assembly project file SCF format." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002055 ! Sequence assembly format
 
 
@@ -28370,7 +29408,7 @@ is_a: EDAM:0002055 ! Sequence assembly format
 id: EDAM:0001633
 name: PHD assembly project file
 namespace: format
-def: "Sequence assembly project file in PHD format." [EDAM:EBI "EMBRACE definition"]
+def: "Sequence assembly project file PHD format." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002055 ! Sequence assembly format
 
 
@@ -28393,7 +29431,7 @@ is_a: EDAM:0002056 ! Microarray experiment data format
 id: EDAM:0001641
 name: EXP file format
 namespace: format
-def: "Affymetrix data file of information about experimental conditions and protocols." [EDAM:EBI "EMBRACE definition"]
+def: "Affymetrix data file format for information about experimental conditions and protocols." [EDAM:EBI "EMBRACE definition"]
 synonym: "Affymetrix experimental conditions data file format" EXACT []
 is_a: EDAM:0002056 ! Microarray experiment data format
 ! relationship: has_source EDAM:0000814 ! ArrayExpress database
@@ -28420,7 +29458,7 @@ id: EDAM:0001644
 name: CHP file format
 namespace: format
 def: "Format of Affymetrix data file of information about (normalised) expression levels of the individual probes." [EDAM:EBI "EMBRACE definition"]
-synonym: "Affymetrix probe normalised data format"  EXACT []
+synonym: "Affymetrix probe normalised data format" EXACT []
 is_a: EDAM:0002058 ! Gene expression report format
 
 [Term]
@@ -28493,7 +29531,7 @@ is_a: EDAM:0002060 ! Map format
 id: EDAM:0001627
 name: Primer3 primer report format
 namespace: format
-def: "Report on PCR primers and hybridization oligos generated by Whitehead primer3 program." [EDAM:EBI "EMBRACE definition"]
+def: "Report format on PCR primers and hybridization oligos as generated by Whitehead primer3 program." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002061 ! Primer report format
 
 
@@ -28519,7 +29557,7 @@ def: "Format of an entry from IntEnz (The Integrated Relational Enzyme Database)
 comment: IntEnz is the master copy of the Enzyme Nomenclature, the recommendations of the NC-IUBMB on the Nomenclature and Classification of Enzyme-Catalysed Reactions.
 is_a: EDAM:0002063 ! Enzyme annotation format
 ! relationship: has_source EDAM:0000822 ! IntEnz database
-! relationship: has_identifier EDAM:0001011 ! Enzyme Commission number
+! relationship: has_identifier EDAM:0001011 ! EC number
 
 [Term]
 id: EDAM:0001512
@@ -28528,7 +29566,25 @@ namespace: format
 def: "Format of an entry from the BRENDA enzyme database." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002063 ! Enzyme annotation format
 ! relationship: has_source EDAM:0000823 ! BRENDA database
-! relationship: has_identifier EDAM:0001011 ! Enzyme Commission number
+! relationship: has_identifier EDAM:0001011 ! EC number
+
+[Term]
+id: EDAM:0002322
+name: BioCyc enzyme report format
+namespace: format
+def: "Format of an entry from the BioCyc enzyme database." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0002063 ! Enzyme annotation format
+! relationship: has_source EDAM:0000823 ! BRENDA database
+! relationship: has_identifier EDAM:0001011 ! EC number
+
+[Term]
+id: EDAM:0002323
+name: ENZYME enzyme report format
+namespace: format
+def: "Format of an entry from the Enzyme nomenclature database (ENZYME)." [EDAM:EBI "EMBRACE definition"]
+is_a: EDAM:0002063 ! Enzyme annotation format
+! relationship: has_source EDAM:0000823 ! BRENDA database
+! relationship: has_identifier EDAM:0001011 ! EC number
 
 [Term]
 id: EDAM:0001513
@@ -28548,7 +29604,7 @@ namespace: format
 def: "Format of an entry from the KEGG ENZYME database." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002063 ! Enzyme annotation format
 ! relationship: has_source EDAM:0000825 ! KEGG ENZYME database
-! relationship: has_identifier EDAM:0001011 ! Enzyme Commission number
+! relationship: has_identifier EDAM:0001011 ! EC number
 ! relationship: has_identifier EDAM:0001154 ! KEGG object identifier
 
 
@@ -28559,7 +29615,7 @@ namespace: format
 def: "Format of an entry from the proto section of the REBASE enzyme database." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002063 ! Enzyme annotation format
 ! relationship: has_source EDAM:0000826 ! REBASE database
-! relationship: has_identifier EDAM:0001011 ! Enzyme Commission number
+! relationship: has_identifier EDAM:0001011 ! EC number
 
 
 [Term]
@@ -28569,7 +29625,7 @@ namespace: format
 def: "Format of an entry from the withrefm section of the REBASE enzyme database." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002063 ! Enzyme annotation format
 ! relationship: has_source EDAM:0000826 ! REBASE database
-! relationship: has_identifier EDAM:0001011 ! Enzyme Commission number
+! relationship: has_identifier EDAM:0001011 ! EC number
 
 
 !
@@ -28706,7 +29762,7 @@ is_a: EDAM:0002068 ! Sequence motif format
 id: EDAM:0001357
 name: EMBOSS sequence pattern
 namespace: format
-def: "EMBOSS sequence pattern." [EDAM:EBI "EMBRACE definition"]
+def: "Format of an EMBOSS sequence pattern." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002068 ! Sequence motif format
 ! relationship: has_source EDAM:0000598 ! Sequence motif or profile data resource
 ! relationship: has_identifier EDAM:0001065 ! Sequence signature identifier
@@ -28775,7 +29831,7 @@ is_a: EDAM:0002072 ! Hidden Markov model format
 id: EDAM:0001349
 name: HMMER Dirichlet prior record
 namespace: format
-def: "Dirichlet distribution in HMMER format." [EDAM:EBI "EMBRACE definition"]
+def: "Dirichlet distribution HMMER format." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002074 ! Dirichlet distribution format
 
 
@@ -28783,7 +29839,7 @@ is_a: EDAM:0002074 ! Dirichlet distribution format
 id: EDAM:0001350
 name: MEME Dirichlet prior record
 namespace: format
-def: "Dirichlet distribution in MEME format." [EDAM:EBI "EMBRACE definition"]
+def: "Dirichlet distribution MEME format." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002074 ! Dirichlet distribution format
 
 
@@ -28817,7 +29873,7 @@ is_a: EDAM:0002077 ! Protein secondary structure format
 id: EDAM:0001455
 name: HSSP entry format
 namespace: format
-def: "An entry from the HSSP database (Homology-derived Secondary Structure in Proteins)." [EDAM:EBI "EMBRACE definition"]
+def: "Entry format of the HSSP database (Homology-derived Secondary Structure in Proteins)." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002077 ! Protein secondary structure format
 ! relationship: is_attribute_of EDAM:0000025 ! Polypeptide
 ! relationship: has_source EDAM:0000705 ! HSSP database
@@ -28860,7 +29916,7 @@ is_a: EDAM:0002078 ! Sequence range format
 id: EDAM:0001295
 name: quicktandem repeat sequence map format
 namespace: format
-def: "Report on tandem repeats in a nucleotide sequence in format generated by the Sanger Centre quicktandem program." [EDAM:EBI "EMBRACE definition"]
+def: "Report format for tandem repeats in a nucleotide sequence (format generated by the Sanger Centre quicktandem program)." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002155 ! Repeat sequence map format
 
 
@@ -28868,7 +29924,7 @@ is_a: EDAM:0002155 ! Repeat sequence map format
 id: EDAM:0001296
 name: Sanger inverted repeat sequence map format
 namespace: format
-def: "Report on inverted repeats in a nucleotide sequence in format generated by the Sanger Centre inverted program." [EDAM:EBI "EMBRACE definition"]
+def: "Report format for inverted repeats in a nucleotide sequence (format generated by the Sanger Centre inverted program)." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002155 ! Repeat sequence map format
 
 
@@ -28876,7 +29932,7 @@ is_a: EDAM:0002155 ! Repeat sequence map format
 id: EDAM:0001297
 name: EMBOSS repeat sequence map format
 namespace: format
-def: "Report on tandem repeats in a sequence in an EMBOSS report format." [EDAM:EBI "EMBRACE definition"]
+def: "Report format for tandem repeats in a sequence (an EMBOSS report format)." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002155 ! Repeat sequence map format
 
 !
@@ -28983,7 +30039,7 @@ is_a: EDAM:0002175 ! Gene cluster format
 id: EDAM:0001639
 name: Affymetrix gene cluster format
 namespace: format
-def: "Fromat of affymetrix gene cluster files (hc-genes.txt, hc-chips.txt) from hierarchical clustering." [EDAM:EBI "EMBRACE definition"]
+def: "Format of affymetrix gene cluster files (hc-genes.txt, hc-chips.txt) from hierarchical clustering." [EDAM:EBI "EMBRACE definition"]
 is_a: EDAM:0002175 ! Gene cluster format
 
 !
@@ -29014,4 +30070,4 @@ id: EDAM:0002211
 name: CIP strain data format
 namespace: format
 def: "Format for a report of strain data as used for CIP database entries." [EDAM:EBI "EMBRACE definition"]
-is_a: EDAM:0002210 ! Strain data format
\ No newline at end of file
+is_a: EDAM:0002210 ! Strain data format