diff --git a/releases/EDAM.obo b/releases/EDAM.obo index 730d5ef..11bef53 100644 --- a/releases/EDAM.obo +++ b/releases/EDAM.obo @@ -1,7 +1,7 @@ format-version: 1.2 -data-version: 1.0 -date: 13:01:2012 18:00 ! Always GMT (UTC) or British Summer Time -saved-by: Matus Kalas +data-version: 1.1 +date: 05:07:2012 18:00 ! Always GMT (UTC) or British Summer Time +saved-by: Jon Ison subsetdef: operations "EDAM operations" !{note="Singular, bioinformatics-specific operations that are functions of tools, workflows, or scripts, or can be performed manually."} subsetdef: data "EDAM types of data" !{note="Types of data that are relevant in bioinformatics, commonly used as inputs, outputs, or intermediate data of analyses, or provided by databases and portals."} subsetdef: topics "EDAM topics" !{note="Application domains of bioinformatics tools and resources; topics of research, studies, or analyses; approaches, techniques, and paradigms within - or directly related to - bioinformatics."} @@ -17,14 +17,8 @@ idspace: EDAM http://edamontology.org/ "EDAM Relations and Concept Attributes" default-relationship-id-prefix: EDAM remark: EDAM (EMBRACE Data And Methods) is an ontology of bioinformatics operations (tool, application, or workflow functions), types of data, topics (application domains), and data formats. The applications of EDAM are within organising tools and data, finding suitable tools in catalogues, and integrating them into complex applications or workflows. Semantic annotations with EDAM are applicable to diverse entities such as for example Web services, databases, programmatic libraries, standalone tools and toolkits, interactive applications, data schemas, data sets, or publications within bioinformatics. Annotation with EDAM may also contribute to data provenance, and EDAM terms and synonyms can be used in text mining. EDAM - and in particular the EDAM Data sub-ontology - serves also as a markup vocabulary for bioinformatics data on the Semantic Web. remark: EDAM editors: Jon Ison and Matus Kalas. Co-authors: Inge Jonassen, Hamish McWilliam, James Malone, Rodrigo Lopez, Helen Parkinson, Steve Pettifer, and Peter Rice. Funding: No funding targetted exclusively the development of EDAM; contibutions from these projects: EMBRACE (FP6, EU), EMBOSS (BBSRC, UK), eSysbio and FUGE Bioinformatics Platform (both Research Council of Norway). See http://edamontology.org for documentation and licence. -remark: NB.! This is a version for the NCBO BioPortal with all attribute modifiers commented out (due to a current problem at BioPortal). Download the full, canonical version from http://edamontology.org/ontology?format=obo (always the latest stable version) or http://edamontology.org/EDAM_1.0.obo (version 1.0). - - - - - - - +next_id:3234 !{since=1.2} +remark: NB. This is a version for the NCBO BioPortal with all attribute modifiers commented out (due to a problem at BioPortal). Download the full, canonical version from http://edamontology.org/ontology?format=obo (always the latest stable version), or http://edamontology.org/EDAM.obo for latest stable and http://edamontology.org/EDAM_1.1.obo for version 1.1. @@ -380,17 +374,17 @@ synonym: "Computational tool" RELATED [http://edamontology.org] !{note="Computat synonym: "Operation" EXACT [http://wsio.org/operation_001] synonym: "function" BROAD [http://purl.org/biotop/biotop.owl#Function] !{note="Operation is a function that has input(s) and output(s) that are data. In addition, one may think of 'biotop:Disposition' (parent of 'biotop:Function') being also a 'biotop:Quality'."} synonym: "function" BROAD [http://semanticscience.org/resource/SIO_000017] -synonym: "continuant" BROAD [snap:Continuant] +synonym: "continuant" BROAD [http://purl.obolibrary.org/obo/BFO_00000??, http://www.ifomis.org/bfo/1.1/snap#Continuant] synonym: "Function" BROAD [http://www.onto-med.de/ontologies/gfo.owl#Function] !{note="However, operation is not a GFO 'Concept' present only in someone's mind."} synonym: "Subroutine" NARROW [http://en.wikipedia.org/wiki/Subroutine, http://en.wikipedia.org/wiki/Function_(computer_science)] synonym: "Function (mathematics)" NARROW [http://en.wikipedia.org/wiki/Function_(mathematics)] synonym: "function" RELATED [sumo:Function] ! Related external synonyms in EDAM without a note is usually almost exact. synonym: "Perpetuant" RELATED [http://www.onto-med.de/ontologies/gfo.owl#Perpetuant] !{note="GFO 'Perpetuant' is in general broader than operation, but it may be seen narrower in the sense of being a concrete individual and exhibiting presentials."} -synonym: "function" RELATED [snap:Function] !{note="BFO 'function' is narrower in the sense that it is a 'realizable_entity' (snap:RealizableEntity) and a 'dependent_continuant' (snap:DependentContinuant), and broader in the sense that it does not need to have input(s) and output(s)."} +synonym: "function" RELATED [http://purl.obolibrary.org/obo/BFO_0000034, http://www.ifomis.org/bfo/1.1/snap#Function] !{note="BFO 'function' is narrower in the sense that it is a 'realizable_entity' (snap:RealizableEntity) and a 'dependent_continuant' (snap:DependentContinuant), and broader in the sense that it does not need to have input(s) and output(s)."} synonym: "quality" RELATED [http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality] !{note="Function, including an operation, can be a quality/attribute of e.g. a computational tool."} -synonym: "quality" RELATED [snap:Quality] !{note="Function, including an operation, can have a role of a quality/attribute in semantic annotation of e.g. a computational tool."} +synonym: "quality" RELATED [http://purl.obolibrary.org/obo/BFO_0000019, http://www.ifomis.org/bfo/1.1/snap#Quality] !{note="Function, including an operation, can have a role of a quality/attribute in semantic annotation of e.g. a computational tool."} synonym: "process" RELATED [http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#process] !{note="Process can have a function (as its quality/attribute), and can also have (perform) an operation with inputs and outputs."} -synonym: "process" RELATED [span:Process] !{note="Process can have a function (as its quality/attribute), and can also have (perform) an operation with inputs and outputs."} +synonym: "process" RELATED [http://purl.obolibrary.org/obo/BFO_00000??, http://www.ifomis.org/bfo/1.1/span#Process] !{note="Process can have a function (as its quality/attribute), and can also have (perform) an operation with inputs and outputs."} synonym: "Process" RELATED [http://www.onto-med.de/ontologies/gfo.owl#Process] !{note="Process can have a function (as its quality/attribute), and can also have (perform) an operation with inputs and outputs."} synonym: "information processing" RELATED [http://www.ebi.ac.uk/swo/SWO_0000003] !{note="However, one may think that an operation is not a process."} synonym: "information processing" RELATED [http://semanticscience.org/resource/SIO_000649] !{note="However, one may think that an operation is not a process and not a physical entity."} @@ -411,7 +405,7 @@ synonym: "Datum" EXACT [http://edamontology.org] !{note="The multiplicity is not synonym: "Data record" EXACT [http://edamontology.org] !{note="Currently we are for practical purposes not distinguishing a data record (a tool-understandable information artefact) from data or datum (its content, the tool-understandable information)."} synonym: "Data set" EXACT [http://edamontology.org] !{note="The multiplicity is not taken into account."} synonym: "Data" EXACT [http://wsio.org/data_002] -synonym: "continuant" BROAD [snap:Continuant] +synonym: "continuant" BROAD [http://purl.obolibrary.org/obo/BFO_00000??, http://www.ifomis.org/bfo/1.1/snap#Continuant] synonym: "digital entity" RELATED [http://purl.org/biotop/biotop.owl#DigitalEntity] synonym: "Perpetuant" RELATED [http://www.onto-med.de/ontologies/gfo.owl#Perpetuant] !{note="GFO 'Perpetuant' is in general broader than data, but it may be seen narrower in the sense of being a concrete individual."} synonym: "data item" RELATED [http://semanticscience.org/resource/SIO_000069] !{note="Data does theoretically not need to have a purpose, but in all regular cases it does. Remark: EDAM Data sub-ontology focuses on scientific data (SIO_000472), in particular the bioinformatics (SIO_010065) and biological (SIO_010019)."} @@ -428,13 +422,13 @@ namespace: topic subset: topics def: "A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other." [http://edamontology.org] synonym: "quality" BROAD [http://purl.org/biotop/biotop.owl#Quality] -synonym: "continuant" BROAD [snap:Continuant] +synonym: "continuant" BROAD [http://purl.obolibrary.org/obo/BFO_00000??, http://www.ifomis.org/bfo/1.1/snap#Continuant] synonym: "field of study" RELATED [sumo:FiledOfStudy] ! Related external synonym in EDAM without a note is usually almost exact. synonym: "Area of Research" RELATED [http://bioontology.org/ontologies/ResearchArea.owl#Area_of_Research] synonym: "Category" RELATED [http://www.onto-med.de/ontologies/gfo.owl#Category] !{note="GFO 'Category' is in general broader than topic, but it may be seen narrower in the sense that it can be instantiated."} synonym: "Perpetuant" RELATED [http://www.onto-med.de/ontologies/gfo.owl#Perpetuant] !{note="GFO 'Perpetuant' is in general broader than topic, but depending on metaphysical (non-)beliefs it may be seen narrower in the sense of being a concrete individual and exhibiting presentials."} synonym: "Method" RELATED [http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Method] -synonym: "quality" RELATED [snap:Quality] !{note="BFO 'quality' is narrower in the sense that it is a 'dependent_continuant' (snap:DependentContinuant), and broader in the sense that it is any quality not just the topic."} +synonym: "quality" RELATED [http://purl.obolibrary.org/obo/BFO_0000019, http://www.ifomis.org/bfo/1.1/snap#Quality] !{note="BFO 'quality' is narrower in the sense that it is a 'dependent_continuant' (snap:DependentContinuant), and broader in the sense that it is any quality not just the topic."} synonym: "quality" RELATED [http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality] !{note="Topic can be a quality of an entity."} @@ -448,7 +442,7 @@ synonym: "Data format" EXACT [http://edamontology.org] synonym: "File format" NARROW [http://edamontology.org] !{note="File format denotes only formats of a computer file, but the same formats apply also to data blobs or messages. Thus the synonym is in practical terms exact."} synonym: "Format" BROAD [http://purl.org/dc/elements/1.1/format] synonym: "quality" BROAD [http://purl.org/biotop/biotop.owl#Quality] -synonym: "continuant" BROAD [snap:Continuant] +synonym: "continuant" BROAD [http://purl.obolibrary.org/obo/BFO_00000??, http://www.ifomis.org/bfo/1.1/snap#Continuant] synonym: "data format specification" RELATED [http://purl.obolibrary.org/obo/IAO_0000098] !{note="Closely related concept focusing on the specification of a data format."} synonym: "Perpetuant" RELATED [http://www.onto-med.de/ontologies/gfo.owl#Perpetuant] !{note="GFO 'Perpetuant' is in general broader than format, but it may be seen narrower in the sense of being a concrete individual and in the way of exhibiting presentials."} synonym: "Symbol structure" RELATED [http://www.onto-med.de/ontologies/gfo.owl#Symbol_structure] @@ -457,7 +451,7 @@ synonym: "machine language" RELATED [http://purl.org/biotop/biotop.owl#MachineLa synonym: "Compression and encoding" RELATED [http://wsio.org/compression_004] !{note="'Compression and encoding' defines additional 'formatting' and/or encoding on top of the primary format."} synonym: "standard" RELATED [http://semanticscience.org/resource/SIO_000618] synonym: "representation" RELATED [http://semanticscience.org/resource/SIO_000612] -synonym: "quality" RELATED [snap:Quality] !{note="BFO 'quality' is narrower in the sense that it is a 'dependent_continuant' (snap:DependentContinuant), and broader in the sense that it is any quality not just the data format."} +synonym: "quality" RELATED [http://purl.obolibrary.org/obo/BFO_0000019, http://www.ifomis.org/bfo/1.1/snap#Quality] !{note="BFO 'quality' is narrower in the sense that it is a 'dependent_continuant' (snap:DependentContinuant), and broader in the sense that it is any quality not just the data format."} synonym: "quality" RELATED [http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality] !{note="Format can be a quality of a data record."} relationship: is_format_of EDAM_data:0006 ! Data ! Unfortunately, OBO-Edit2 doesn't show the subject concept at the top level when browsed with the 'f' option. @@ -586,6 +580,27 @@ is_a: EDAM_topic:0078 ! Protein analysis [Term] +id: EDAM_topic:3174 !{since=1.1} +name: Metagenomics +namespace: topic +subset: topics +def: "Topic concerning the study of genetic material recovered from environmental samples." [http://edamontology.org] +synonym: "Environmental genomics" EXACT [http://edamontology.org] +synonym: "Ecogenomics" EXACT [http://edamontology.org] +synonym: "Community genomics" EXACT [http://edamontology.org] +is_a: EDAM_topic:0610 ! Ecoinformatics +is_a: EDAM_topic:0622 ! Genomics + + +[Term] +id: EDAM_topic:3172 !{since=1.1} +name: Metabolomics +namespace: topic +subset: topics +def: "Topic concerning the study of metabolites and the chemical processes they are involved in, especially the systematic study of the chemical fingerprints of specific cellular processes." [http://edamontology.org] +is_a: EDAM_topic:0003 ! Topic + +[Term] id: EDAM_topic:0079 name: Metabolites namespace: topic @@ -593,6 +608,7 @@ subset: topics def: "Topic concerning the reactants or products of metabolism, for example small molecules such as including vitamins, polyols, nucleotides and amino acids." [http://edamontology.org] comment: This concept excludes macromolecules such as proteins and nucleic acids. is_a: EDAM_topic:0154 ! Small molecules +is_a: EDAM_topic:3172 ! Metabolomics [Term] id: EDAM_topic:0080 @@ -692,10 +708,10 @@ is_a: EDAM_topic:0003 ! Topic [Term] id: EDAM_topic:0200 -! alt_id: EDAM_topic:0206 name: Microarrays namespace: topic subset: topics +! alt_id: EDAM_topic:0206 def: "Topic concerning microarrays, for example, to process microarray data or design probes and experiments." [http://edamontology.org] xref: BioCatalogue:Microarrays synonym: "DNA microarrays" EXACT [http://edamontology.org] @@ -735,6 +751,15 @@ xref: BioCatalogue:Structural Genomics is_a: EDAM_topic:2226 ! Structure determination is_a: EDAM_topic:0622 ! Genomics +[Term] +id: EDAM_topic:3173 !{since=1.1} +name: Epigenomics +namespace: topic +subset: topics +def: "A topic concerning the study of the epigenetic modifications of a whole cell, tissue, organism etc." [http://edamontology.org] +comment: Epigenetics concerns the heritable changes in gene expression owing to mechanisms other than DNA sequence variation. +synonym: "Epigenetics" EXACT [http://edamontology.org] +is_a: EDAM_topic:0622 ! Genomics @@ -775,12 +800,12 @@ is_a: EDAM_topic:2829 ! Ontologies, nomenclature and classification [Term] id: EDAM_topic:0090 -! alt_id: EDAM_topic:0155 -! alt_id: EDAM_topic:2274 -! alt_id: EDAM_topic:0165 name: Data search and retrieval namespace: topic subset: topics +! alt_id: EDAM_topic:0155 +! alt_id: EDAM_topic:2274 +! alt_id: EDAM_topic:0165 def: "Topic concerning the search and query of data sources (typically biological databases or ontologies) in order to retrieve entries or other information." [http://edamontology.org] comment: This includes, for example, search, query and retrieval of molecular sequences and associated data. synonym: "Data retrieval" EXACT [http://edamontology.org] @@ -923,6 +948,7 @@ subset: topics def: "Topic that aims to identify, predict, model or analyse genes or gene structure in DNA sequences." [http://edamontology.org] comment: This includes the study of promoters, coding regions, splice sites, etc. 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 [http://edamontology.org] +synonym: "Gene discovery" EXACT [http://edamontology.org] xref: BioCatalogue:Gene Prediction is_a: EDAM_topic:3073 ! Nucleic acid feature detection @@ -1005,6 +1031,7 @@ namespace: topic subset: topics ! alt_id: EDAM_topic:0587 def: "Topic concerning protein-protein, protein-DNA/RNA and protein-ligand interactions, including analysis of known interactions and prediction of putative interactions." [http://edamontology.org] +comment: This includes experimental (e.g. yeast two-hybrid) and computational analysis techniques. xref: BioCatalogue:Protein Interaction is_a: EDAM_topic:1775 ! Protein function analysis is_a: EDAM_topic:2225 ! Protein databases @@ -1198,11 +1225,11 @@ is_a: EDAM_topic:0080 ! Sequence analysis [Term] id: EDAM_topic:0158 -! alt_id: EDAM_topic:0161 -! alt_id: EDAM_topic:0162 name: Sequence motifs namespace: topic subset: topics +! alt_id: EDAM_topic:0161 +! alt_id: EDAM_topic:0162 def: "Topic concerning conserved patterns (motifs) in molecular sequences, that (typically) describe functional or other key sites." [http://edamontology.org] synonym: "Motifs" EXACT [http://edamontology.org] is_a: EDAM_topic:0594 ! Sequence classification @@ -1445,6 +1472,7 @@ subset: topics def: "Topic concerning the prediction of secondary or supersecondary structure of protein sequences." [http://edamontology.org] xref: BioCatalogue:Protein Secondary Structure is_a: EDAM_topic:0172 ! Protein structure prediction +is_a: EDAM_topic:0694 ! Protein secondary structure [Term] id: EDAM_topic:0179 @@ -1454,6 +1482,7 @@ subset: topics def: "Topic concerning the prediction of tertiary structure of protein sequences." [http://edamontology.org] xref: BioCatalogue:Protein Tertiary Structure is_a: EDAM_topic:0172 ! Protein structure prediction +is_a: EDAM_topic:0698 ! Protein tertiary structure [Term] id: EDAM_topic:0180 @@ -1488,6 +1517,18 @@ is_a: EDAM_topic:3041 ! Sequence databases [Term] +id: EDAM_topic:3178 +name: RNA-Seq alignment +namespace: topic +subset: topics +def: "Topic concerning the alignment of sequences of (typically millions) of short reads to a reference genome. This is a specialised topic within sequence alignment, especially because of complications arising from RNA splicing." [http://edamontology.org] +synonym: "RNA-seq alignment" EXACT [http://edamontology.org] +is_a: EDAM_topic:0182 ! Sequence alignment + + + + +[Term] id: EDAM_topic:0183 ! alt_id: EDAM_topic:2272 ! alt_id: EDAM_topic:2273 @@ -1555,7 +1596,7 @@ subset: topics def: "Topic concerning parallelized sequencing processes that are capable of sequencing many thousands of sequences simultaneously." [http://edamontology.org] synonym: "Next-generation sequencing" EXACT [http://edamontology.org] is_obsolete: true !{since=beta13} -consider: EDAM_topic:0102 ! Sequencing and mapping +consider: EDAM_topic:3168 ! Sequencing [Term] id: EDAM_topic:0195 @@ -1574,7 +1615,7 @@ name: Sequence assembly namespace: topic subset: topics def: "Topic concerning the assembly of fragments of a DNA sequence to reconstruct the original sequence." [http://edamontology.org] -is_a: EDAM_topic:0102 ! Sequencing and mapping +is_a: EDAM_topic:3168 ! Sequencing [Term] @@ -1614,24 +1655,74 @@ consider: EDAM_topic:0200 ! Microarrays [Term] id: EDAM_topic:0102 -name: Sequencing and mapping +name: Mapping +namespace: topic +subset: topics +def: "Topic concerning the mapping of complete (typically nucleotide) sequences." [http://edamontology.org] +is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis + +[Term] +id: EDAM_topic:3168 !{since=1.1} +name: Sequencing namespace: topic subset: topics -def: "Topic concerning the determination and mapping of complete (typically nucleotide) sequences." [http://edamontology.org] +def: "Topic concerning the determination of complete (typically nucleotide) sequences, including those of genomes (full genome sequencing, de novo sequencing and resequencing), amplicons and transcriptomes." [http://edamontology.org] is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis [Term] -id: EDAM_topic:0197 -name: Gene expression resources +id: EDAM_topic:3169 !{since=1.1} +name: ChIP-seq namespace: topic subset: topics -def: "Topic concerning primarily raw or processed gene expression (typically microarray) data." [http://edamontology.org] -comment: This includes microarray data, northern blots, gene-indexed expression profiles and any annotation on genetic information that is used in the synthesis of a protein. -is_a: EDAM_topic:2816 ! Gene resources +def: "Topic concerning the analysis of protein-DNA interactions where chromatin immunoprecipitation (ChIP) is used in combination with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins." [http://edamontology.org] +synonym: "Chip-sequencing" EXACT [http://edamontology.org] +synonym: "Chip sequencing" EXACT [http://edamontology.org] +synonym: "Chip seq" EXACT [http://edamontology.org] +is_a: EDAM_topic:3168 ! Sequencing +is_a: EDAM_topic:0128 ! Protein interactions + +[Term] +id: EDAM_topic:3179 !{since=1.1} +name: ChIP-on-chip +namespace: topic +subset: topics +def: "Topic concerning experimental techniques that combine chromatin immunoprecipitation ('ChIP') with microarray ('chip'). ChIP-on-chip is used for high-throughput study protein-DNA interactions." [http://edamontology.org] +synonym: "ChIP-chip" EXACT [http://edamontology.org] +is_a: EDAM_topic:3168 ! Sequencing +is_a: EDAM_topic:0128 ! Protein interactions + + + +[Term] +id: EDAM_topic:3170 !{since=1.1} +name: RNA-Seq +namespace: topic +subset: topics +def: "A topic concerning high-throughput sequencing of cDNA to measure the RNA content (transcriptome) of a sample, for example, to investigate how different alleles of a gene are expressed, detect post-transcriptional mutations or identify gene fusions. " [http://edamontology.org] +comment: This includes small RNA profiling (small RNA-Seq), for example to find novel small RNAs, characterize mutations and analyze expression of small RNAs. +synonym: "RNA-seq" EXACT [http://edamontology.org] +synonym: "Small RNA-Seq" EXACT [http://edamontology.org] +synonym: "Small RNA-seq" EXACT [http://edamontology.org] +synonym: "Whole transcriptome shotgun sequencing" EXACT [http://edamontology.org] +synonym: "WTSS" EXACT [http://edamontology.org] +is_a: EDAM_topic:3168 ! Sequencing is_a: EDAM_topic:0203 ! Transcriptomics + + + +[Term] +id: EDAM_topic:3177 !{since=1.1} +name: DNA-Seq +namespace: topic +subset: topics +def: "A topic concerning high-throughput sequencing of randomly fragmented genomic DNA, for example, to investigate whole-genome sequencing and resequencing, SNP discovery, identification of copy number variations and chromosomal rearrangements." [http://edamontology.org] +synonym: "DNA-seq" EXACT [http://edamontology.org] +is_a: EDAM_topic:3168 ! Sequencing + + [Term] id: EDAM_topic:3062 !{since=beta13} name: Genetic organisation @@ -1645,12 +1736,13 @@ is_a: EDAM_topic:2816 ! Gene resources [Term] id: EDAM_topic:0204 -name: Gene regulation resources +name: Gene regulation namespace: topic subset: topics ! alt_id: EDAM_topic:3049 ! alt_id: EDAM_topic:0631 def: "Topic concerning primarily the regulation of gene expression." [http://edamontology.org] +synonym: "Gene regulation resources" EXACT [http://edamontology.org] is_a: EDAM_topic:2816 ! Gene resources @@ -1663,7 +1755,7 @@ subset: topics def: "Topic concerning DNA sequence variation (mutation and polymorphism) data." [http://edamontology.org] synonym: "Mutation and polymorphism" EXACT [http://edamontology.org] synonym: "DNA variation" EXACT [http://edamontology.org] -is_a: EDAM_topic:0625 ! Genotype and phenotype resources +is_a: EDAM_topic:0625 ! Genotype and phenotype is_a: EDAM_topic:3041 ! Sequence databases is_a: EDAM_topic:0640 ! Nucleic acid sequence analysis @@ -1681,10 +1773,15 @@ id: EDAM_topic:0203 name: Transcriptomics namespace: topic subset: topics -def: "Topic concerning the analysis of mRNA expression levels, by identifying, quantifying or comparing mRNA transcripts or interpreting (in functional terms) gene expression data." [http://edamontology.org] +alt_id: EDAM_topic:0197 +def: "Topic concerning primarily raw or processed gene (mRNA) expression (typically microarray) data, including the analysis of gene expression levels, by identifying, quantifying or comparing mRNA transcripts and the interpretation (in functional terms) of gene expression data." [http://edamontology.org] +comment: This includes microarray data, northern blots, gene-indexed expression profiles and any annotation on genetic information that is used in the synthesis of a protein. synonym: "Gene expression profiling" EXACT [http://edamontology.org] synonym: "Expression profiling" EXACT [http://edamontology.org] +synonym: "Gene expression resources" EXACT [http://edamontology.org] +synonym: "Gene expression analysis" EXACT [http://edamontology.org] is_a: EDAM_topic:0003 ! Topic +is_a: EDAM_topic:2816 ! Gene resources [Term] @@ -1692,7 +1789,7 @@ id: EDAM_topic:2277 name: SNPs namespace: topic subset: topics -def: "Topic concerning single nucleotide polymorphisms (SNP) and associated data." [http://edamontology.org] +def: "Topic concerning single nucleotide polymorphisms (SNP) and associated data, for example, the discovery and annotation of SNPs." [http://edamontology.org] comment: A SNP is a DNA sequence variation where a single nucleotide differs between members of a species or paired chromosomes in an individual. is_a: EDAM_topic:0199 ! Genetic variation @@ -1818,10 +1915,10 @@ is_a: EDAM_topic:0217 ! Literature analysis [Term] id: EDAM_topic:0219 -! alt_id: EDAM_topic:2256 name: Annotation namespace: topic subset: topics +! alt_id: EDAM_topic:2256 def: "Topic for the annotation of entities (typically biological database entries) with terms from a controlled vocabulary." [http://edamontology.org] synonym: "Ontology annotation" EXACT [http://edamontology.org] xref: BioCatalogue:Genome Annotation @@ -1983,15 +2080,18 @@ id: EDAM_topic:0602 name: Pathways, networks and models namespace: topic subset: topics +alt_id: EDAM_topic:3076 !{since=beta13} ! alt_id: EDAM_topic:0198 ! alt_id: EDAM_topic:0755 -def: "Topic concerning biological pathways, networks and other models." [http://edamontology.org] +def: "Topic concerning biological pathways, networks and other models, including their construction and analysis." [http://edamontology.org] +synonym: "Network or pathway analysis" EXACT [http://edamontology.org] xref: BioCatalogue:Pathways xref: BioCatalogue:Pathway Retrieval is_a: EDAM_topic:2259 ! Systems biology is_a: EDAM_topic:3071 ! Biological data resources + [Term] id: EDAM_topic:3075 !{since=beta13} name: Biological system modelling @@ -2002,13 +2102,6 @@ xref: BioCatalogue:Model Analysis xref: BioCatalogue:Model Execution is_a: EDAM_topic:2259 ! Systems biology -[Term] -id: EDAM_topic:3076 !{since=beta13} -name: Network or pathway analysis -namespace: topic -subset: topics -def: "The processing (including construction) and analysis of biological networks and pathways." [http://edamontology.org] -is_a: EDAM_topic:2259 ! Systems biology [Term] @@ -2190,7 +2283,7 @@ comment: General information on or more organisms, genomes (including molecular synonym: "Genome map" EXACT [http://edamontology.org] is_a: EDAM_topic:0622 ! Genomics is_a: EDAM_topic:0121 ! Proteomics -is_a: EDAM_topic:0625 ! Genotype and phenotype resources +is_a: EDAM_topic:0625 ! Genotype and phenotype [Term] id: EDAM_topic:0622 @@ -2267,15 +2360,28 @@ subset: topics def: "Topic concerning chromosomes." [http://edamontology.org] is_a: EDAM_topic:3062 ! Genetic organisation +[Term] +id: EDAM_topic:3175 !{since=1.1} +name: Structural variation +namespace: topic +subset: topics +def: "Topic concerning variation in chromosome structure including microscopic and submicroscopic types of variation such as deletions, duplications, copy-number variants, insertions, inversions and translocations." [http://edamontology.org] +synonym: "Genomic structural variation" EXACT [http://edamontology.org] +is_a: EDAM_topic:0624 ! Chromosomes +is_a: EDAM_topic:0199 ! Genetic variation + + [Term] id: EDAM_topic:0625 -name: Genotype and phenotype resources +name: Genotype and phenotype namespace: topic subset: topics ! alt_id: EDAM_topic:2231 def: "Topic concerning the study of genetic constitution of a living entity, such as an individual, and organism, a cell and so on, typically with respect to a particular observable phenotypic traits, or resources concerning such traits, which might be an aspect of biochemistry, physiology, morphology, anatomy, development and so on." [http://edamontology.org] +synonym: "Genotyping" EXACT [http://edamontology.org] +synonym: "Genotype and phenotype resources" EXACT [http://edamontology.org] is_a: EDAM_topic:2816 ! Gene resources [Term] @@ -2307,7 +2413,7 @@ namespace: topic subset: topics def: "Topic concerning gene expression e.g. microarray data, northern blots, gene-indexed expression profiles etc." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_topic:0197 ! Gene expression resources +consider: EDAM_topic:0203 ! Transcriptomics consider: EDAM_topic:0200 ! Microarrays @@ -2317,7 +2423,7 @@ name: Disease resources namespace: topic subset: topics def: "Topic concerning diseases." [http://edamontology.org] -is_a: EDAM_topic:0625 ! Genotype and phenotype resources +is_a: EDAM_topic:0625 ! Genotype and phenotype [Term] id: EDAM_topic:2813 @@ -2442,23 +2548,46 @@ subset: topics ! alt_id: EDAM_topic:0628 def: "Topic concerning DNA sequences and structure, including processes such as methylation and replication." [http://edamontology.org] comment: The DNA sequences might be coding or non-coding sequences. +synonym: "DNA analysis" EXACT [http://edamontology.org] is_a: EDAM_topic:3042 ! Nucleic acid sequences +is_a: EDAM_topic:0077 ! Nucleic acid analysis + +[Term] +id: EDAM_topic:3176 +name: DNA packaging +namespace: topic +subset: topics +def: "Topic concerning DNA-histone complexes (chromatin), organisation of chromatin into nucleosomes and packaging into higher-order structures." [http://edamontology.org] +is_a: EDAM_topic:0654 ! DNA +is_a: EDAM_topic:0624 ! Chromosomes + + +[Term] +id: EDAM_topic:3171 !{since=1.1} +name: DNA methylation +namespace: topic +subset: topics +def: "Topic concerning DNA methylation including bisulfite sequencing, methylation sites and analysis, for example of patterns and profiles of DNA methylation in a population, tissue etc." [http://edamontology.org] +is_a: EDAM_topic:0654 ! DNA + [Term] id: EDAM_topic:0655 -name: mRNA, EST or cDNA +name: mRNA, EST or cDNA database namespace: topic subset: topics ! alt_id: EDAM_topic:0205 -def: "Topic concerning messenger RNA (mRNA), expressed sequence tag (EST) or complementary DNA (cDNA) sequences." [http://edamontology.org] +def: "Topic concerning data resources for messenger RNA (mRNA), expressed sequence tag (EST) or complementary DNA (cDNA) sequences." [http://edamontology.org] synonym: "Transcriptome" EXACT [http://edamontology.org] +synonym: "Transcriptome database" EXACT [http://edamontology.org] +synonym: "mRNA, EST or cDNA" EXACT [http://edamontology.org] is_a: EDAM_topic:0099 ! RNA [Term] id: EDAM_topic:0659 -name: Functional RNA +name: Functional and non-coding RNA namespace: topic subset: topics ! alt_id: EDAM_topic:0113 @@ -2468,8 +2597,11 @@ subset: topics ! alt_id: EDAM_topic:0120 def: "Topic concerning functional or non-coding RNA sequences." [http://edamontology.org] comment: For example, piwi-interacting RNA (piRNA), small nuclear RNA (snRNA) and small nucleolar RNA (snoRNA). +synonym: "Non-coding RNA" EXACT [http://edamontology.org] +synonym: "Functional RNA" EXACT [http://edamontology.org] is_a: EDAM_topic:0099 ! RNA + [Term] id: EDAM_topic:3060 !{since=beta13} name: Regulatory RNA @@ -2481,7 +2613,7 @@ subset: topics ! alt_id: EDAM_topic:0118 def: "Topic concerning regulatory RNA sequences including microRNA (miRNA) and small interfering RNA (siRNA)." [http://edamontology.org] comment: Micro RNAs are short single stranded RNA molecules that regulate gene expression. -is_a: EDAM_topic:0659 ! Functional RNA +is_a: EDAM_topic:0659 ! Functional and non-coding RNA [Term] @@ -2491,7 +2623,7 @@ namespace: topic subset: topics ! alt_id: EDAM_topic:0116 def: "Topic concerning one or more ribosomal RNA (rRNA) sequences." [http://edamontology.org] -is_a: EDAM_topic:0659 ! Functional RNA +is_a: EDAM_topic:0659 ! Functional and non-coding RNA [Term] @@ -2501,7 +2633,7 @@ namespace: topic subset: topics ! alt_id: EDAM_topic:0115 def: "Topic concerning one or more transfer RNA (tRNA) sequences." [http://edamontology.org] -is_a: EDAM_topic:0659 ! Functional RNA +is_a: EDAM_topic:0659 ! Functional and non-coding RNA [Term] @@ -2511,16 +2643,11 @@ namespace: topic subset: topics ! alt_id: EDAM_topic:0126 ! alt_id: EDAM_topic:0590 +alt_id: EDAM_topic:3040 !{since=beta13} def: "Topic concerning protein secondary or tertiary structural data and/or associated annotation." [http://edamontology.org] +synonym: "Protein structure" EXACT [http://edamontology.org] is_a: EDAM_topic:0078 ! Protein analysis is_a: EDAM_topic:0081 ! Structure analysis - -[Term] -id: EDAM_topic:3040 !{since=beta13} -name: Protein structure -namespace: topic -subset: topics -def: "Topic concerning protein secondary or tertiary structural data and/or associated annotation." [http://edamontology.org] is_a: EDAM_topic:3038 ! Structure databases is_a: EDAM_topic:2225 ! Protein databases @@ -2534,7 +2661,7 @@ subset: topics def: "Topic concerning protein secondary structure or secondary structure alignments." [http://edamontology.org] comment: This includes assignment, analysis, comparison, prediction, rendering etc. of secondary structure data. synonym: "Protein secondary structure analysis" EXACT [http://edamontology.org] -is_a: EDAM_topic:3040 ! Protein structure +is_a: EDAM_topic:2814 ! Protein structure analysis [Term] id: EDAM_topic:0698 @@ -2543,7 +2670,8 @@ namespace: topic subset: topics ! alt_id: EDAM_topic:2125 def: "Topic concerning protein tertiary structures." [http://edamontology.org] -is_a: EDAM_topic:3040 ! Protein structure +synonym: "Protein tertiary structure analysis" EXACT [http://edamontology.org] +is_a: EDAM_topic:2814 ! Protein structure analysis @@ -2732,7 +2860,7 @@ comment: This includes promoters, enhancers, silencers and boundary elements / i synonym: "Transcriptional regulatory sites" EXACT [http://edamontology.org] synonym: "Transcription factors" EXACT [http://edamontology.org] synonym: "Transcription factor and binding site" EXACT [http://edamontology.org] -is_a: EDAM_topic:0204 ! Gene regulation resources +is_a: EDAM_topic:0204 ! Gene regulation is_a: EDAM_topic:0110 ! Transcription is_a: EDAM_topic:0635 ! Specific protein resources is_a: EDAM_topic:0747 ! Nucleic acid sites and features @@ -2760,6 +2888,8 @@ namespace: topic subset: topics def: "Topic concerning metabolic pathways." [http://edamontology.org] is_a: EDAM_topic:0602 ! Pathways, networks and models +is_a: EDAM_topic:3172 ! Metabolomics + [Term] id: EDAM_topic:0754 @@ -2798,7 +2928,7 @@ namespace: topic subset: topics def: "Topic concerning gene regulatory networks." [http://edamontology.org] is_a: EDAM_topic:0602 ! Pathways, networks and models -is_a: EDAM_topic:0204 ! Gene regulation resources +is_a: EDAM_topic:0204 ! Gene regulation [Term] @@ -3060,7 +3190,7 @@ subset: topics def: "Informatics resources that aim to identify, map or analyse genetic markers in DNA sequences, for example to produce a genetic (linkage) map of a chromosome or genome or to analyse genetic linkage and synteny." [http://edamontology.org] synonym: "Genetic linkage" EXACT [http://edamontology.org] synonym: "Linkage mapping" EXACT [http://edamontology.org] -is_a: EDAM_topic:0102 ! Sequencing and mapping +is_a: EDAM_topic:0102 ! Mapping relationship: has_topic EDAM_topic:3053 ! Genetics @@ -3070,7 +3200,7 @@ name: Comparative genomics namespace: topic subset: topics ! alt_id: EDAM_topic:0101 -def: "Topic for the study (typically comparison) of the structure or function of multiple genomes." [http://edamontology.org] +def: "Topic concerning the study (typically comparison) of the sequence, structure or function of multiple genomes." [http://edamontology.org] xref: BioCatalogue:Comparative Genomics is_a: EDAM_topic:0622 ! Genomics @@ -3111,7 +3241,7 @@ subset: topics ! alt_id: EDAM_topic:0633 def: "Topic for the application of information technology to immunology such as immunological processes, immunological genes, proteins and peptide ligands, antigens and so on." [http://edamontology.org] synonym: "Computational immunology" EXACT [http://edamontology.org] -is_a: EDAM_topic:0003 ! Topics +is_a: EDAM_topic:0003 ! Topic [Term] id: EDAM_topic:2830 @@ -3136,11 +3266,12 @@ consider: EDAM_topic:0634 ! Disease resources [Term] id: EDAM_topic:2640 -name: Cancer resources +name: Cancer namespace: topic subset: topics ! alt_id: EDAM_topic:0805 def: "Informatics resources dedicated to the study of cancer, for example, genes and proteins implicated in cancer." [http://edamontology.org] +synonym: "Cancer resources" EXACT [http://edamontology.org] is_a: EDAM_topic:0634 ! Disease resources @@ -3219,8 +3350,8 @@ def: "Process (read and / or write) data of a specific type, for example applyin synonym: "Calculation" EXACT [http://edamontology.org] synonym: "Computation" EXACT [http://edamontology.org] is_a: EDAM_operation:0004 ! Operation -relationship: has_input EDAM_data:0006 ! Data ! !{min_cardinality=0} -relationship: has_output EDAM_data:0006 ! Data ! !{min_cardinality=0} +relationship: has_input EDAM_data:0006 !{min_cardinality=0} ! Data +relationship: has_output EDAM_data:0006 !{min_cardinality=0} ! Data [Term] id: EDAM_operation:2423 @@ -3292,7 +3423,7 @@ namespace: operation subset: operations def: "Analyse known protein-protein, protein-DNA/RNA or protein-ligand interactions." [http://edamontology.org] is_a: EDAM_operation:2405 ! Protein interaction data processing -relationship: has_output EDAM_data:0906 !{min_cardinality=1} ! Protein report (interaction) +relationship: has_output EDAM_data:0906 !{min_cardinality=1} ! Protein interaction relationship: has_topic EDAM_topic:0128 ! Protein interactions @@ -3313,7 +3444,6 @@ namespace: operation subset: operations def: "Compare two or more entities, typically the sequence or structure (or derivatives) of macromolecules, to identify equivalent subunits." [http://edamontology.org] synonym: "Alignment" EXACT [http://edamontology.org] -is_a: EDAM_operation:0004 ! Operation is_a: EDAM_operation:2951 ! Alignment processing relationship: has_output EDAM_data:1916 !{min_cardinality=1} ! Alignment @@ -3428,7 +3558,8 @@ subset: operations def: "Map properties to positions on an biological entity (typically a molecular sequence or structure), or assemble such an entity from constituent parts." [http://edamontology.org] comment: This is a broad concept and is used a placeholder for other, more specific concepts. is_a: EDAM_operation:0004 ! Operation -relationship: has_topic EDAM_topic:0102 ! Sequencing and mapping +relationship: has_topic EDAM_topic:0102 ! Mapping +relationship: has_topic EDAM_topic:0196 ! Sequence assembly [Term] id: EDAM_operation:2430 @@ -3457,7 +3588,7 @@ subset: operations def: "Search or query a data resource and retrieve entries and / or annotation." [http://edamontology.org] synonym: "Database retrieval" EXACT [http://edamontology.org] is_a: EDAM_operation:0004 ! Operation -relationship: has_output EDAM_data:0006 ! Data ! !{min_cardinality=0} +relationship: has_output EDAM_data:0006 !{min_cardinality=0} ! Data relationship: has_topic EDAM_topic:0090 ! Data search and retrieval [Term] @@ -3467,8 +3598,8 @@ namespace: operation subset: operations def: "Process (read and / or write) nucleic acid sequence or structural data." [http://edamontology.org] is_a: EDAM_operation:2420 ! Analysis and processing -relationship: has_input EDAM_data:2084 ! Nucleic acid report ! !{min_cardinality=0} -relationship: has_output EDAM_data:2084 ! Nucleic acid report ! !{min_cardinality=0} +relationship: has_input EDAM_data:2084 !{min_cardinality=0} ! Nucleic acid report +relationship: has_output EDAM_data:2084 !{min_cardinality=0} ! Nucleic acid report relationship: has_topic EDAM_topic:0077 ! Nucleic acid analysis @@ -3479,8 +3610,8 @@ namespace: operation subset: operations def: "Process (read and / or write) protein sequence or structural data." [http://edamontology.org] is_a: EDAM_operation:2420 ! Analysis and processing -relationship: has_input EDAM_data:0896 ! Protein report ! !{min_cardinality=0} -relationship: has_output EDAM_data:0896 ! Protein report ! !{min_cardinality=0} +relationship: has_input EDAM_data:0896 !{min_cardinality=0} ! Protein report +relationship: has_output EDAM_data:0896 !{min_cardinality=0} ! Protein report relationship: has_topic EDAM_topic:0078 ! Protein analysis @@ -3501,8 +3632,8 @@ namespace: operation subset: operations def: "Process (read and / or write) an alignment of two or more molecular sequences, structures or derived data." [http://edamontology.org] is_a: EDAM_operation:2420 ! Analysis and processing -relationship: has_input EDAM_data:1916 ! Alignment ! !{min_cardinality=0} -relationship: has_output EDAM_data:1916 ! Alignment ! !{min_cardinality=0} +relationship: has_input EDAM_data:1916 !{min_cardinality=0} ! Alignment +relationship: has_output EDAM_data:1916 !{min_cardinality=0} ! Alignment @@ -3514,8 +3645,8 @@ subset: operations def: "Process (read and / or write) an index of (typically a file of) biological data." [http://edamontology.org] synonym: "Database index processing" EXACT [http://edamontology.org] is_a: EDAM_operation:2409 ! File processing -relationship: has_input EDAM_data:0955 ! Data index ! !{min_cardinality=0} -relationship: has_output EDAM_data:0955 ! Data index ! !{min_cardinality=0} +relationship: has_input EDAM_data:0955 !{min_cardinality=0} ! Data index +relationship: has_output EDAM_data:0955 !{min_cardinality=0} ! Data index relationship: has_topic EDAM_topic:0220 ! Data processing and validation [Term] @@ -3558,8 +3689,8 @@ namespace: operation subset: operations def: "Process (read and / or write) molecular sequence motifs." [http://edamontology.org] is_a: EDAM_operation:2420 ! Analysis and processing -relationship: has_input EDAM_data:1353 ! Sequence motif ! !{min_cardinality=0} -relationship: has_output EDAM_data:1353 ! Sequence motif ! !{min_cardinality=0} +relationship: has_input EDAM_data:1353 !{min_cardinality=0} ! Sequence motif +relationship: has_output EDAM_data:1353 !{min_cardinality=0} ! Sequence motif relationship: has_topic EDAM_topic:0158 ! Sequence motifs @@ -3678,8 +3809,8 @@ namespace: operation subset: operations def: "Process (read and / or write) protein interaction data." [http://edamontology.org] is_a: EDAM_operation:2502 ! Protein data processing -relationship: has_input EDAM_data:0906 ! Protein report (interaction) ! !{min_cardinality=0} -relationship: has_output EDAM_data:0906 ! Protein report (interaction) ! !{min_cardinality=0} +relationship: has_input EDAM_data:0906 !{min_cardinality=0} ! Protein interaction +relationship: has_output EDAM_data:0906 !{min_cardinality=0} ! Protein interaction relationship: has_topic EDAM_topic:0128 ! Protein interactions [Term] @@ -3690,11 +3821,100 @@ subset: operations def: "Process (read and / or write) a DNA map of some type." [http://edamontology.org] synonym: "DNA map data processing" EXACT [http://edamontology.org] is_a: EDAM_operation:2501 ! Nucleic acid data processing -relationship: has_input EDAM_data:1274 ! Map ! !{min_cardinality=0} -relationship: has_output EDAM_data:1274 ! Map ! !{min_cardinality=0} +relationship: has_input EDAM_data:1274 !{min_cardinality=0} ! Map +relationship: has_output EDAM_data:1274 !{min_cardinality=0} ! Map relationship: has_topic EDAM_topic:0796 ! Genetic mapping and linkage + +[Term] +id: EDAM_operation:3229 !{since=1.1} +name: Exome analysis +namespace: operation +subset: operations +def: "Anaylse sequencing data from experiments aiming to selectively sequence the coding regions of the genome." [http://edamontology.org] +comment: Exome sequencing is considered a cheap alternative to whole genome sequencing. +synonym: "Exome sequence analysis" EXACT [http://edamontology.org] +synonym: "Targeted exome capture" EXACT [http://edamontology.org] +is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis + + +[Term] +id: EDAM_operation:3230 !{since=1.1} +name: Read depth analysis +namespace: operation +subset: operations +def: "Analyse mapping density (read depth) of (typically) short reads from sequencing platforms, for example, to detect deletions and duplications." [http://edamontology.org] +is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis + + +[Term] +id: EDAM_operation:3225 !{since=1.1} +name: Variant classification +namespace: operation +subset: operations +def: "Classify variants based on their potential effect on genes, especially functional effects on the expressed proteins." [http://edamontology.org] +comment: Variants are typically classified by their position (intronic, exonic, etc.) in a gene transcript and (for variants in coding exons) by their effect on the protein sequence (synonymous, non-synonymous, frameshifting, etc.) +is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis +is_a: EDAM_operation:2995 ! Sequence classification + +[Term] +id: EDAM_operation:3226 !{since=1.1} +name: Variant prioritization +namespace: operation +subset: operations +def: "Identify biologically interesting variants by prioritizing individual variants, for example, homozygous variants absent in control genomes." [http://edamontology.org] +comment: Variant prioritization can be used for example to produce a list of variants responsible for 'knocking out' genes in specific genomes. Methods amino acid substitution, aggregative approaches, probabilistic approach, inheritance and unified likelihood-frameworks. +is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis + +[Term] +id: EDAM_operation:3221 !{since=1.1} +name: Species frequency estimation +namespace: operation +subset: operations +def: "Estimate the frequencies of different species from analysis of the molecular sequences, typically of DNA recovered from environmental samples." [http://edamontology.org] +is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis +relationship: has_topic EDAM_topic:3174 ! Metagenomics + + + +[Term] +id: EDAM_operation:3216 !{since=1.1} +name: Scaffolding +namespace: operation +subset: operations +def: "Link together a non-contiguous series of genomic sequences into a scaffold, consisting of sequences separated by gaps of known length. The sequences that are linked are typically typically contigs; contiguous sequences corresponding to read overlaps." [http://edamontology.org] +comment: Scaffold may be positioned along a chromosome physical map to create a "golden path". +synonym: "Scaffold construction" EXACT [http://edamontology.org] +is_a: EDAM_operation:2429 ! Mapping and assembly +is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) +is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis + +[Term] +id: EDAM_operation:3217 !{since=1.1} +name: Scaffold gap completion +namespace: operation +subset: operations +def: "Fill the gaps in a sequence assembly (scaffold) by merging in additional sequences." [http://edamontology.org] +comment: Different techniques are used to generate gap sequences to connect contigs, depending on the size of the gap. For small (5-20kb) gaps, PCR amplification and sequencing is used. For large (>20kb) gaps, fragments are cloned (e.g. in BAC (Bacterial artificial chromosomes) vectors) and then sequenced. +is_a: EDAM_operation:2429 ! Mapping and assembly +is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) +is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis + + + +[Term] +id: EDAM_operation:3218 !{since=1.1} +name: Sequencing quality control +namespace: operation +subset: operations +def: "Raw sequence data quality control." [http://edamontology.org] +synonym: "Sequencing QC" EXACT [http://edamontology.org] +synonym: "Analyse raw sequence data from a sequencing pipeline and identify problems." EXACT [http://edamontology.org] +is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis +is_a: EDAM_operation:2428 ! Evaluation and validation + + [Term] id: EDAM_operation:2520 name: DNA mapping @@ -3728,7 +3948,7 @@ subset: operations def: "Generate a physical (sequence) map of a DNA sequence showing the physical distance (base pairs) between features or landmarks such as restriction sites, cloned DNA fragments, genes and other genetic markers." [http://edamontology.org] is_a: EDAM_operation:2520 ! DNA mapping relationship: has_output EDAM_data:1280 !{min_cardinality=1} ! Physical map -relationship: has_topic EDAM_topic:0102 ! Sequencing and mapping +relationship: has_topic EDAM_topic:0102 ! Mapping [Term] @@ -3742,6 +3962,29 @@ synonym: "Sequence mapping" EXACT [http://edamontology.org] is_a: EDAM_operation:2944 ! Physical mapping relationship: has_output EDAM_data:1279 !{min_cardinality=1} ! Sequence map + + +[Term] +id: EDAM_operation:3233 !{since=1.1} +name: Copy number estimation +namespace: operation +subset: operations +def: "Estimate the number of copies of loci of particular gene(s) in DNA sequences typically from gene-expression profiling technology based on microarray hybridization-based experiments. For example, estimate copy number (or marker dosage) of a dominant marker in samples from polyploid plant cells or tissues, or chromosomal gains and losses in tumors." [http://edamontology.org] +comment: Methods typically implement some statistical model for hypothesis testing, and methods estimate total copy number, i.e. do not distinguish the two inherited chromosomes quantities (specific copy number). +synonym: "Transcript copy number estimation" EXACT [http://edamontology.org] +is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis + +[Term] +id: EDAM_operation:3219 !{since=1.1} +name: Read pre-processing +namespace: operation +subset: operations +def: "Pre-process sequence reads to ensure (or improve) quality and reliability." [http://edamontology.org] +comment: This is a broad concept and is used a placeholder for other, more specific concepts. For example process paired end reads to trim low quality ends remove short sequences, identify sequence inserts, detect chimeric reads, or remove low quality sequnces including vector, adaptor, low complexity and contaminant sequences. Sequences might come from genomic DNA library, EST libraries, SSH library and so on. +synonym: "Sequence read pre-processing" EXACT [http://edamontology.org] +is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis + + [Term] id: EDAM_operation:0283 name: Linkage analysis @@ -3781,8 +4024,8 @@ namespace: operation subset: operations def: "Process (read and / or write) a molecular sequence alignment." [http://edamontology.org] is_a: EDAM_operation:2951 ! Alignment processing -relationship: has_input EDAM_data:0863 ! Sequence alignment ! !{min_cardinality=0} -relationship: has_output EDAM_data:0863 ! Sequence alignment ! !{min_cardinality=0} +relationship: has_input EDAM_data:0863 !{min_cardinality=0} ! Sequence alignment +relationship: has_output EDAM_data:0863 !{min_cardinality=0} ! Sequence alignment relationship: has_topic EDAM_topic:0182 ! Sequence alignment [Term] @@ -3792,8 +4035,8 @@ namespace: operation subset: operations def: "Process (read and / or write) a molecular tertiary (3D) structure alignment." [http://edamontology.org] is_a: EDAM_operation:2951 ! Alignment processing -relationship: has_input EDAM_data:0886 ! Structure alignment ! !{min_cardinality=0} -relationship: has_output EDAM_data:0886 ! Structure alignment ! !{min_cardinality=0} +relationship: has_input EDAM_data:0886 !{min_cardinality=0} ! Structure alignment +relationship: has_output EDAM_data:0886 !{min_cardinality=0} ! Structure alignment relationship: has_topic EDAM_topic:0183 ! Structure alignment @@ -3809,7 +4052,7 @@ synonym: "Sequence alignment generation" EXACT [http://edamontology.org] is_a: EDAM_operation:2463 ! Sequence alignment processing !(?) is_a: EDAM_operation:2451 ! Sequence comparison is_a: EDAM_operation:2928 ! Alignment construction -relationship: has_input EDAM_data:2044 !{min_cardinality=2, note="Applies to both pure/raw sequences and sequence records. Indirectly also to sequence sets or IDs (?)"} ! Sequence +relationship: has_input EDAM_data:2044 !{minCardinality=2, note="Applies to both pure/raw sequences and sequence records. Indirectly also to sequence sets or IDs (?)"} ! Sequence relationship: has_output EDAM_data:0863 !{min_cardinality=1} ! Sequence alignment relationship: has_topic EDAM_topic:0182 ! Sequence alignment @@ -3821,7 +4064,7 @@ subset: operations def: "Align two or more molecular sequences of different types (for example genomic DNA to EST, cDNA or mRNA)." [http://edamontology.org] synonym: "Hybrid sequence alignment" EXACT [http://edamontology.org] is_obsolete: true !{since=beta13} -consider: EDAM_operation:0292 ! Sequence alignment +consider: EDAM_operation:0292 ! Sequence alignment construction [Term] id: EDAM_operation:0294 @@ -3876,7 +4119,7 @@ namespace: operation subset: operations def: "Align (superimpose) molecular tertiary structures." [http://edamontology.org] synonym: "Structure alignment" EXACT [http://edamontology.org] -is_a: EDAM_operation:2928 ! Alignment +is_a: EDAM_operation:2928 ! Alignment construction is_a: EDAM_operation:2483 ! Structure comparison is_a: EDAM_operation:2952 ! Structure alignment processing relationship: has_output EDAM_data:0886 !{min_cardinality=1} ! Structure alignment @@ -3889,8 +4132,8 @@ namespace: operation subset: operations def: "Process (read and / or write) some type of sequence profile." [http://edamontology.org] is_a: EDAM_operation:2420 ! Analysis and processing -relationship: has_input EDAM_data:1354 ! Sequence profile ! !{min_cardinality=0} -relationship: has_output EDAM_data:1354 ! Sequence profile ! !{min_cardinality=0} +relationship: has_input EDAM_data:1354 !{min_cardinality=0} ! Sequence profile +relationship: has_output EDAM_data:1354 !{min_cardinality=0} ! Sequence profile relationship: has_topic EDAM_topic:0188 ! Sequence profiles and HMMs [Term] @@ -3900,8 +4143,8 @@ namespace: operation subset: operations def: "Process (read and / or write) one or more structural (3D) profile(s) or template(s) of some type." [http://edamontology.org] is_a: EDAM_operation:2420 ! Analysis and processing -relationship: has_input EDAM_data:0889 ! Structural (3D) profile ! !{min_cardinality=0} -relationship: has_output EDAM_data:0889 ! Structural (3D) profile ! !{min_cardinality=0} +relationship: has_input EDAM_data:0889 !{min_cardinality=0} ! Structural (3D) profile +relationship: has_output EDAM_data:0889 !{min_cardinality=0} ! Structural (3D) profile relationship: has_topic EDAM_topic:0167 ! Structural (3D) profiles @@ -3914,7 +4157,7 @@ def: "Recognize (predict and identify) known protein structural domains or folds 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 [http://edamontology.org] synonym: "Protein fold prediction" EXACT [http://edamontology.org] -is_a: EDAM_operation:0414 ! Protein feature detection (from sequence) +is_a: EDAM_operation:0414 ! Protein feature prediction (from sequence) is_a: EDAM_operation:0474 ! Protein structure prediction is_a: EDAM_operation:2997 ! Protein comparison relationship: has_output EDAM_data:0901 !{min_cardinality=1} ! Protein features (domains) @@ -3935,8 +4178,8 @@ namespace: operation subset: operations def: "Process (read and / or write) text." [http://edamontology.org] is_a: EDAM_operation:2420 ! Analysis and processing -relationship: has_input EDAM_data:2048 ! Report ! !{min_cardinality=0} -relationship: has_output EDAM_data:2048 ! Report ! !{min_cardinality=0} +relationship: has_input EDAM_data:2048 !{min_cardinality=0} ! Report +relationship: has_output EDAM_data:2048 !{min_cardinality=0} ! Report [Term] id: EDAM_operation:0306 @@ -3946,7 +4189,7 @@ subset: operations def: "Process and analyse text (typically the biomedical and informatics literature) to extract information from it." [http://edamontology.org] synonym: "Text data mining" EXACT [http://edamontology.org] is_a: EDAM_operation:2947 ! Article analysis -relationship: has_input EDAM_data:2048 ! Report ! !{min_cardinality=0} +relationship: has_input EDAM_data:2048 !{min_cardinality=0} ! Report relationship: has_output EDAM_data:0972 ! Text mining report relationship: has_topic EDAM_topic:0218 ! Text mining @@ -3966,15 +4209,29 @@ id: EDAM_operation:0310 name: Sequence assembly namespace: operation subset: operations -def: "Assemble fragments of a DNA sequence to reconstruct the original sequence." [http://edamontology.org] -comment: Typically, contigs (for example ESTs and genomic DNA fragments) are aligned and merged, depending on the detected fragment overlaps. Annotation of the assembled sequence might be generated. +def: "Combine (align and merge) overlapping fragments of a DNA sequence to reconstruct the original sequence." [http://edamontology.org] +comment: For example, assemble overlapping reads from paired-end sequencers into contigs (a contiguous sequence corresponding to read overlaps). Or assemble contigs, for example ESTs and genomic DNA fragments, depending on the detected fragment overlaps. is_a: EDAM_operation:2429 ! Mapping and assembly -is_a: EDAM_operation:2446 ! Sequence processing +is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis relationship: has_output EDAM_data:0925 ! Sequence assembly relationship: has_topic EDAM_topic:0196 ! Sequence assembly [Term] +id: EDAM_operation:3180 !{since=1.1} +name: Sequence assembly evaluation +namespace: operation +subset: operations +def: "Evaluate a DNA sequence assembly, typically for purposes of quality control." [http://edamontology.org] +is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) +is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis +is_a: EDAM_operation:2425 ! Optimisation and refinement +relationship: has_input EDAM_data:0925 ! Sequence assembly +relationship: has_output EDAM_data:3181 ! Sequence assembly report +relationship: has_topic EDAM_topic:0196 ! Sequence assembly + + +[Term] id: EDAM_operation:2432 name: Microarray data processing namespace: operation @@ -3992,9 +4249,9 @@ def: "Process (read and / or write) gene expression (typically microarray) data. is_a: EDAM_operation:2420 ! Analysis and processing synonym: "Gene expression (microarray) data processing" EXACT [http://edamontology.org] synonym: "Microarray data processing" EXACT [http://edamontology.org] -relationship: has_input EDAM_data:3117 ! Microarray hybridisation data ! !{min_cardinality=0} -relationship: has_output EDAM_data:3117 ! Microarray hybridisation data ! !{min_cardinality=0} -relationship: has_topic EDAM_topic:0197 ! Gene expression resources +relationship: has_input EDAM_data:3117 !{min_cardinality=0} ! Microarray hybridisation data +relationship: has_output EDAM_data:3117 !{min_cardinality=0} ! Microarray hybridisation data +relationship: has_topic EDAM_topic:0203 ! Transcriptomics relationship: has_topic EDAM_topic:0200 ! Microarrays @@ -4016,8 +4273,8 @@ def: "Standardize or normalize microarray data." [http://edamontology.org] comment: This includes statistical analysis, for example of variability amongst microarrays experiments, comparison of heterogeneous microarray platforms etc. is_a: EDAM_operation:2495 ! Gene expression data processing is_a: EDAM_operation:2428 ! Evaluation and validation -relationship: has_input EDAM_data:3117 !{min_cardinality=1} ! Microarray hybridisation data -relationship: has_output EDAM_data:3117 !{min_cardinality=1} ! Microarray hybridisation data +relationship: has_input EDAM_data:3117 !{min_cardinality=1} ! Microarray hybridisation data +relationship: has_output EDAM_data:3117 !{min_cardinality=1} ! Microarray hybridisation data [Term] id: EDAM_operation:0318 @@ -4072,8 +4329,8 @@ namespace: operation subset: operations def: "Generate, analyse or handle a biological pathway or network." [http://edamontology.org] is_a: EDAM_operation:2420 ! Analysis and processing -relationship: has_input EDAM_data:2600 ! Pathway or network ! !{min_cardinality=0} -relationship: has_output EDAM_data:2600 ! Pathway or network ! !{min_cardinality=0} +relationship: has_input EDAM_data:2600 !{min_cardinality=0} ! Pathway or network +relationship: has_output EDAM_data:2600 !{min_cardinality=0} ! Pathway or network relationship: has_topic EDAM_topic:0602 ! Pathways, networks and models [Term] @@ -4088,6 +4345,16 @@ relationship: has_input EDAM_data:2600 !{min_cardinality=1} ! Pathway or network relationship: has_topic EDAM_topic:0602 ! Pathways, networks and models +[Term] +id: EDAM_operation:3203 !{since=1.1} +name: Chromatogram visualisation +namespace: operation +subset: operations +def: "Visualise, format or render an image of a Chromatogram." [http://edamontology.org] +synonym: "Chromatogram viewing" EXACT [http://edamontology.org] +is_a: EDAM_operation:0337 ! Plotting and rendering + + [Term] @@ -4096,6 +4363,8 @@ name: Pathway or network analysis namespace: operation subset: operations def: "Analyse a known biological pathway or network." [http://edamontology.org] +synonym: "Network analysis" EXACT [http://edamontology.org] +synonym: "Pathway analysis" EXACT [http://edamontology.org] is_a: EDAM_operation:2438 ! Pathway or network processing relationship: has_input EDAM_data:2600 !{min_cardinality=1} ! Pathway or network relationship: has_output EDAM_data:2984 !{min_cardinality=1} ! Pathway or network report @@ -4147,8 +4416,8 @@ synonym: "Report handling" EXACT [http://edamontology.org] synonym: "File handling" EXACT [http://edamontology.org] synonym: "Data file processing" EXACT [http://edamontology.org] is_a: EDAM_operation:2420 ! Analysis and processing -relationship: has_input EDAM_data:0006 ! Data ! !{min_cardinality=0} -relationship: has_output EDAM_data:0006 ! Data ! !{min_cardinality=0} +relationship: has_input EDAM_data:0006 !{min_cardinality=0} ! Data +relationship: has_output EDAM_data:0006 !{min_cardinality=0} ! Data relationship: has_topic EDAM_topic:0220 ! Data processing and validation @@ -4161,7 +4430,7 @@ def: "Visualise, plot or render (graphically) biomolecular data such as molecula synonym: "Visualisation" EXACT [http://edamontology.org] is_a: EDAM_operation:0004 ! Operation relationship: has_input EDAM_data:0006 !{min_cardinality=1} ! Data -relationship: has_output EDAM_data:2968 ! Image ! !{min_cardinality=0} +relationship: has_output EDAM_data:2968 !{min_cardinality=0} ! Image relationship: has_topic EDAM_topic:0092 ! Data visualisation @@ -4236,6 +4505,8 @@ name: Data loading namespace: operation subset: operations def: "Prepare or load a user-specified data file so that it is available for use." [http://edamontology.org] +synonym: "Database submission" EXACT [http://edamontology.org] +synonym: "Data submission" EXACT [http://edamontology.org] xref: WHATIF:UploadPDB is_a: EDAM_operation:2409 ! File processing relationship: has_input EDAM_data:0842 !{min_cardinality=1} ! Identifier @@ -4268,7 +4539,7 @@ def: "Search a database (or other data resource) with a supplied query and retri comment: Typically the query is compared to each entry and high scoring matches (hits) are returned. For example, a BLAST search of a sequence database. is_a: EDAM_operation:0224 ! Search and retrieval is_a: EDAM_operation:2424 ! Comparison -relationship: has_output EDAM_data:2080 ! Database hits ! !{min_cardinality=0} +relationship: has_output EDAM_data:2080 !{min_cardinality=0} ! Database hits [Term] id: EDAM_operation:2422 @@ -4321,7 +4592,7 @@ comment: This includes direct retrieval methods (e.g. the dbfetch program) but n synonym: "Data retrieval (sequences)" EXACT [http://edamontology.org] is_a: EDAM_operation:2422 ! Data retrieval is_a: EDAM_operation:2446 ! Sequence processing -relationship: has_output EDAM_data:2044 ! Sequence ! !{min_cardinality=0} +relationship: has_output EDAM_data:2044 !{min_cardinality=0} ! Sequence [Term] id: EDAM_operation:1814 @@ -4334,7 +4605,7 @@ xref: WHATIF:DownloadPDB xref: WHATIF:EchoPDB is_a: EDAM_operation:2422 ! Data retrieval is_a: EDAM_operation:2465 ! Structure processing -relationship: has_output EDAM_data:0883 ! Structure ! !{min_cardinality=0} +relationship: has_output EDAM_data:0883 !{min_cardinality=0} ! Structure [Term] @@ -4494,7 +4765,7 @@ def: "Search and retrieve names of or documentation on bioinformatics tools, for synonym: "Tool information retrieval" EXACT [http://edamontology.org] synonym: "Data retrieval (tool annotation)" EXACT [http://edamontology.org] is_a: EDAM_operation:0304 ! Data retrieval (metadata and documentation) -relationship: has_output EDAM_data:0958 ! Tool metadata ! !{min_cardinality=0} +relationship: has_output EDAM_data:0958 !{min_cardinality=0} ! Tool metadata [Term] @@ -4506,7 +4777,7 @@ def: "Search and retrieve names of or documentation on bioinformatics databases synonym: "Database information retrieval" EXACT [http://edamontology.org] synonym: "Data retrieval (database annotation)" EXACT [http://edamontology.org] is_a: EDAM_operation:0304 ! Data retrieval (metadata and documentation) -relationship: has_output EDAM_data:0957 ! Database metadata ! !{min_cardinality=0} +relationship: has_output EDAM_data:0957 !{min_cardinality=0} ! Database metadata [Term] @@ -4543,7 +4814,7 @@ namespace: operation subset: operations def: "Query the biomedical and informatics literature." [http://edamontology.org] is_a: EDAM_operation:2421 ! Database search -relationship: has_output EDAM_data:0970 ! Bibliographic reference ! !{min_cardinality=0} +relationship: has_output EDAM_data:0970 !{min_cardinality=0} ! Bibliographic reference relationship: has_topic EDAM_topic:0217 ! Literature analysis [Term] @@ -4555,7 +4826,7 @@ def: "Search a sequence database by sequence comparison and retrieve similar seq comment: This excludes direct retrieval methods (e.g. the dbfetch program). is_a: EDAM_operation:2421 ! Database search is_a: EDAM_operation:2403 ! Sequence analysis -relationship: has_output EDAM_data:0857 ! Database hits (sequence) ! !{min_cardinality=0} +relationship: has_output EDAM_data:0857 !{min_cardinality=0} ! Database hits (sequence) relationship: has_topic EDAM_topic:0159 ! Sequence comparison @@ -4567,7 +4838,7 @@ subset: operations def: "Search a tertiary structure database by sequence and/or structure comparison and retrieve structures and associated data." [http://edamontology.org] is_a: EDAM_operation:2421 ! Database search is_a: EDAM_operation:2996 ! Structure classification -relationship: has_output EDAM_data:0885 ! Database hits (structure) ! !{min_cardinality=0} +relationship: has_output EDAM_data:0885 !{min_cardinality=0} ! Database hits (structure) relationship: has_topic EDAM_topic:0081 ! Structure analysis [Term] @@ -4580,7 +4851,7 @@ comment: Methods might use fingerprints, profiles, hidden Markov models, sequenc synonym: "Protein sequence classification" EXACT [http://edamontology.org] is_a: EDAM_operation:2421 ! Database search is_a: EDAM_operation:3093 ! Sequence screening -relationship: has_output EDAM_data:0858 ! Database hits (secondary) ! !{min_cardinality=0} +relationship: has_output EDAM_data:0858 !{min_cardinality=0} ! Database hits (secondary) relationship: has_topic EDAM_topic:0595 ! Protein classification [Term] @@ -4592,7 +4863,7 @@ def: "Screen a sequence against a motif or pattern database." [http://edamontolo is_a: EDAM_operation:2421 ! Database search is_a: EDAM_operation:0239 ! Sequence motif recognition is_a: EDAM_operation:3093 ! Sequence screening -relationship: has_output EDAM_data:1298 ! Sequence features (motifs) ! !{min_cardinality=0} +relationship: has_output EDAM_data:1298 !{min_cardinality=0} ! Sequence features (motifs) relationship: has_topic EDAM_topic:0158 ! Sequence motifs [Term] @@ -4602,7 +4873,7 @@ namespace: operation subset: operations def: "Search a database of sequence profiles with a query sequence." [http://edamontology.org] is_a: EDAM_operation:2421 ! Database search -is_a: EDAM_operation:0300 ! Sequence-profile alignment +is_a: EDAM_operation:0300 ! Sequence-profile alignment construction is_a: EDAM_operation:3093 ! Sequence screening relationship: has_output EDAM_data:1298 ! Sequence features (motifs) @@ -4671,7 +4942,7 @@ def: "Search a sequence database and retrieve sequences that are similar to a qu comment: This includes tools based on PSI-BLAST. synonym: "Sequence similarity search (profile-based methods)" EXACT [http://edamontology.org] is_a: EDAM_operation:0346 ! Sequence database search (by sequence) -is_a: EDAM_operation:0300 ! Sequence-profile alignment +is_a: EDAM_operation:0300 ! Sequence-profile alignment construction [Term] id: EDAM_operation:0352 @@ -4682,7 +4953,7 @@ def: "Search a sequence database for sequences that are similar to a query seque comment: This includes tools based on the Smith-Waterman algorithm or FASTA. synonym: "Sequence similarity search (local alignment-based methods) " EXACT [http://edamontology.org] is_a: EDAM_operation:0346 ! Sequence database search (by sequence) -is_a: EDAM_operation:0493 ! Pairwise sequence alignment (local) +is_a: EDAM_operation:0493 ! Pairwise sequence alignment construction (local) relationship: has_topic EDAM_topic:0182 ! Sequence alignment [Term] @@ -4694,7 +4965,7 @@ def: "Search sequence(s) or a sequence database for sequences that are similar t comment: This includes tools based on the Needleman and Wunsch algorithm. synonym: "Sequence similarity search (global alignment-based methods)" EXACT [http://edamontology.org] is_a: EDAM_operation:0346 ! Sequence database search (by sequence) -is_a: EDAM_operation:0494 ! Pairwise sequence alignment (global) +is_a: EDAM_operation:0494 ! Pairwise sequence alignment construction (global) relationship: has_topic EDAM_topic:0182 ! Sequence alignment [Term] @@ -4789,7 +5060,7 @@ def: "Annotate an entity (typically a biological or biomedical database entity) comment: This is a broad concept and is used a placeholder for other, more specific concepts. is_a: EDAM_operation:0004 ! Operation relationship: has_input EDAM_data:0582 ! Ontology -relationship: has_topic EDAM_topic:0089 ! Ontologies +relationship: has_topic EDAM_topic:0089 ! Ontology [Term] @@ -4845,6 +5116,41 @@ synonym: "Database indexing" EXACT [http://edamontology.org] is_a: EDAM_operation:2412 ! Data index processing relationship: has_output EDAM_data:0955 ! Data index + +[Term] +id: EDAM_operation:3211 !{since=1.1} +name: Genome indexing +namespace: operation +subset: operations +def: "Generate an index of a genome sequence." [http://edamontology.org] +comment: Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment. +is_a: EDAM_operation:0227 ! Data indexing +relationship: has_output EDAM_data:3210 ! Genome index + +[Term] +id: EDAM_operation:3212 !{since=1.1} +name: Genome indexing (Burrows-Wheeler) +namespace: operation +subset: operations +def: "Generate an index of a genome sequence using the Burrows-Wheeler algorithm." [http://edamontology.org] +comment: The Burrows-Wheeler Transform (BWT) is a permutation of the genome based on a suffix array algorithm. +synonym: "Burrows-Wheeler" EXACT [http://edamontology.org] +synonym: "Burrows Wheeler" EXACT [http://edamontology.org] +synonym: "Genome indexing (Burrows Wheeler)" EXACT [http://edamontology.org] +is_a: EDAM_operation:3211 ! Genome indexing + +[Term] +id: EDAM_operation:3213 !{since=1.1} +name: Genome indexing (suffix arrays) +namespace: operation +subset: operations +def: "Generate an index of a genome sequence using a suffix arrays algorithm." [http://edamontology.org] +comment: A suffix array consists of the lexicographically sorted list of suffixes of a genome. +synonym: "suffix arrays" EXACT [http://edamontology.org] +is_a: EDAM_operation:3211 ! Genome indexing + + + [Term] id: EDAM_operation:0228 name: Data index analysis @@ -4864,6 +5170,7 @@ name: Nucleic acid sequence analysis namespace: operation subset: operations def: "Analyse a nucleic acid sequence (using methods that are only applicable to nucleic acid sequences)." [http://edamontology.org] +synonym: "Sequence analysis (nucleic acid)" EXACT [http://edamontology.org] is_a: EDAM_operation:2403 ! Sequence analysis is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) relationship: has_input EDAM_data:2977 !{min_cardinality=1} ! Nucleic acid sequence @@ -4888,6 +5195,7 @@ name: Protein sequence analysis namespace: operation subset: operations def: "Analyse a protein sequence (using methods that are only applicable to protein sequences)." [http://edamontology.org] +synonym: "Sequence analysis (protein)" EXACT [http://edamontology.org] is_a: EDAM_operation:2403 ! Sequence analysis is_a: EDAM_operation:2447 ! Sequence processing (protein) synonym: "Sequence analysis (protein)" EXACT [http://edamontology.org] @@ -4897,6 +5205,27 @@ relationship: has_topic EDAM_topic:0639 ! Protein sequence analysis [Term] +id: EDAM_operation:3214 !{since=1.1} +name: Spectrum analysis +namespace: operation +subset: operations +def: "Analyse a spectrum from a mass spectrometry (or other) experiment." [http://edamontology.org] +synonym: "Spectral analysis" EXACT [http://edamontology.org] +synonym: "Mass spectrum analysis" EXACT [http://edamontology.org] +is_a: EDAM_operation:2420 ! Analysis and processing + +[Term] +id: EDAM_operation:3215 !{since=1.1} +name: Peak detection +namespace: operation +subset: operations +def: "Identify peaks in a spectrum from a mass spectrometry experiment." [http://edamontology.org] +synonym: "Peak finding" EXACT [http://edamontology.org] +is_a: EDAM_operation:3214 ! Spectrum analysis +relationship: has_input EDAM_data:0943 !{min_cardinality=1} ! Mass spectrometry spectra + + +[Term] id: EDAM_operation:2446 name: Sequence processing namespace: operation @@ -4905,8 +5234,8 @@ subset: operations def: "Process (read and / or write) one or more molecular sequences and associated annotation." [http://edamontology.org] synonym: "Sequence processing (general)" EXACT [http://edamontology.org] is_a: EDAM_operation:2420 ! Analysis and processing -relationship: has_input EDAM_data:2044 ! Sequence ! !{min_cardinality=0} -relationship: has_output EDAM_data:2044 ! Sequence ! !{min_cardinality=0} +relationship: has_input EDAM_data:2044 !{min_cardinality=0} ! Sequence +relationship: has_output EDAM_data:2044 !{min_cardinality=0} ! Sequence relationship: has_topic EDAM_topic:0080 ! Sequence analysis [Term] @@ -4917,8 +5246,8 @@ subset: operations def: "Process (read and / or write) a protein sequence and associated annotation." [http://edamontology.org] is_a: EDAM_operation:2446 ! Sequence processing is_a: EDAM_operation:2502 ! Protein data processing -relationship: has_input EDAM_data:2976 ! Protein sequence ! !{min_cardinality=0} -relationship: has_output EDAM_data:2976 ! Protein sequence ! !{min_cardinality=0} +relationship: has_input EDAM_data:2976 !{min_cardinality=0} ! Protein sequence +relationship: has_output EDAM_data:2976 !{min_cardinality=0} ! Protein sequence [Term] id: EDAM_operation:2448 @@ -4928,8 +5257,8 @@ subset: operations def: "Process (read and / or write) a nucleotide sequence and associated annotation." [http://edamontology.org] is_a: EDAM_operation:2446 ! Sequence processing is_a: EDAM_operation:2501 ! Nucleic acid data processing -relationship: has_input EDAM_data:2977 ! Nucleic acid sequence ! !{min_cardinality=0} -relationship: has_output EDAM_data:2977 ! Nucleic acid sequence ! !{min_cardinality=0} +relationship: has_input EDAM_data:2977 !{min_cardinality=0} ! Nucleic acid sequence +relationship: has_output EDAM_data:2977 !{min_cardinality=0} ! Nucleic acid sequence [Term] id: EDAM_operation:0229 @@ -5022,7 +5351,7 @@ subset: operations def: "Submit a molecular sequence to a database." [http://edamontology.org] is_a: EDAM_operation:2446 ! Sequence processing relationship: has_input EDAM_data:2044 !{min_cardinality=1} ! Sequence -relationship: has_topic EDAM_topic:0091 ! Data handling +relationship: has_topic EDAM_topic:3077 ! Data acquisition and deposition [Term] id: EDAM_operation:0234 @@ -5061,7 +5390,7 @@ synonym: "Sequence cluster generation" EXACT [http://edamontology.org] is_a: EDAM_operation:2451 ! Sequence comparison is_a: EDAM_operation:2452 ! Sequence cluster processing is_a: EDAM_operation:2995 ! Sequence classification -relationship: has_output EDAM_data:1235 ! Sequence cluster ! !{min_cardinality=0} +relationship: has_output EDAM_data:1235 !{min_cardinality=0} ! Sequence cluster [Term] id: EDAM_operation:0236 @@ -5092,7 +5421,7 @@ namespace: operation subset: operations def: "Compare two or more molecular sequences, identify and remove redundant sequences based on some criteria." [http://edamontology.org] is_a: EDAM_operation:0291 ! Sequence clustering -relationship: has_output EDAM_data:2044 ! Sequence ! !{min_cardinality=0} +relationship: has_output EDAM_data:2044 !{min_cardinality=0} ! Sequence relationship: has_topic EDAM_topic:0164 ! Sequence clustering @@ -5151,6 +5480,62 @@ is_a: EDAM_operation:2451 ! Sequence comparison relationship: has_output EDAM_data:0870 ! Sequence distance matrix relationship: has_topic EDAM_topic:0084 ! Phylogenetics +[Term] +id: EDAM_operation:3200 !{since=1.1} +name: DNA barcoding +namespace: operation +subset: operations +def: "Analyse DNA sequences in order to identify a DNA barcode; short fragment(s) of DNA that are useful to diagnose the taxa of biological organisms." [http://edamontology.org] +synonym: "Sample barcoding" EXACT [http://edamontology.org] +is_a: EDAM_operation:0415 ! Nucleic acid feature prediction + + + +[Term] +id: EDAM_operation:3204 !{since=1.1} +name: Methylation analysis +namespace: operation +subset: operations +def: "Determine cytosine methylation states in nucleic acid sequences." [http://edamontology.org] +is_a: EDAM_operation:0415 ! Nucleic acid feature prediction + +[Term] +id: EDAM_operation:3205 !{since=1.1} +name: Methylation calling +namespace: operation +subset: operations +def: "Determine cytosine methylation status of specific positions in a nucleic acid sequences." [http://edamontology.org] +is_a: EDAM_operation:3204 ! Methylation analysis + +[Term] +id: EDAM_operation:3206 !{since=1.1} +name: Methylation level analysis (global) +namespace: operation +subset: operations +def: "Measure the overall level of methyl cytosines in a genome from analysis of experimental data, typically from chromatographic methods and methyl accepting capacity assay." [http://edamontology.org] +synonym: "Global methylation analysis" EXACT [http://edamontology.org] +is_a: EDAM_operation:3205 ! Methylation calling + +[Term] +id: EDAM_operation:3207 !{since=1.1} +name: Methylation level analysis (gene-specific) +namespace: operation +subset: operations +def: "Measure the level of methyl cytosines in specific genes." [http://edamontology.org] +comment: Many different techniques are available for this. +synonym: "Gene-specific methylation analysis" EXACT [http://edamontology.org] +is_a: EDAM_operation:3205 ! Methylation calling + + +[Term] +id: EDAM_operation:3209 !{since=1.1} +name: Genome comparison +namespace: operation +subset: operations +def: "Compare the sequence or features of two or more genomes, for example, to find matching regions." [http://edamontology.org] +synonym: "Genomic region matching" EXACT [http://edamontology.org] +is_a: EDAM_operation:2508 ! Nucleic acid sequence comparison + [Term] id: EDAM_operation:0266 @@ -5159,7 +5544,7 @@ namespace: operation subset: operations def: "Detect vector sequences in nucleotide sequence, typically by comparison to a set of known vector sequences." [http://edamontology.org] is_a: EDAM_operation:2508 ! Nucleic acid sequence comparison -is_a: EDAM_operation:0415 ! Nucleic acid feature detection +is_a: EDAM_operation:0415 ! Nucleic acid feature prediction [Term] id: EDAM_operation:2233 @@ -5180,6 +5565,29 @@ comment: For example, identify full-length cDNAs from EST sequences or detect po is_obsolete: true !{since=beta12orEarlier} consider: EDAM_operation:2403 ! Sequence analysis +[Term] +id: EDAM_operation:3185 !{since=1.1} +name: Base-calling +namespace: operation +subset: operations +def: "Identify base (nucleobase) sequence from a fluorescence 'trace' data generated by an automated DNA sequencer." [http://edamontology.org] +synonym: "Base calling" EXACT [http://edamontology.org] +synonym: "Phred base calling" EXACT [http://edamontology.org] +synonym: "Phred base-calling" EXACT [http://edamontology.org] +is_a: EDAM_operation:2448 ! Sequence processing (nucleic acid) +relationship: has_topic EDAM_topic:3168 ! Sequencing + + +[Term] +id: EDAM_operation:3195 +name: Sequencing error detection +namespace: operation +subset: operations +def: "Detect errors in DNA sequences generated from sequencing projects)." [http://edamontology.org] +synonym: "Short-read error correction" EXACT [http://edamontology.org] +synonym: "Short read error correction" EXACT [http://edamontology.org] +is_a: EDAM_operation:2508 ! Nucleic acid sequence comparison +relationship: has_topic EDAM_topic:3168 ! Sequencing [Term] id: EDAM_operation:0265 @@ -5188,9 +5596,9 @@ namespace: operation subset: operations def: "Detect frameshift errors in DNA sequences (from sequencing projects)." [http://edamontology.org] comment: Methods include sequence alignment (if related sequences are available) and word-based sequence comparison. -is_a: EDAM_operation:2508 ! Nucleic acid sequence comparison -is_a: EDAM_operation:0415 ! Nucleic acid feature detection -relationship: has_topic EDAM_topic:0102 ! Sequencing and mapping +is_a: EDAM_operation:3195 ! Sequencing error detection +is_a: EDAM_operation:3197 ! Genetic variation analysis +relationship: has_topic EDAM_topic:3168 ! Sequencing [Term] @@ -5212,7 +5620,7 @@ subset: operations def: "Identify genetic markers in DNA sequences." [http://edamontology.org] comment: A genetic marker is any DNA sequence of known chromosomal location that is associated with and specific to a particular gene or trait. This includes short sequences surrounding a SNP, Sequence-Tagged Sites (STS) which are well suited for PCR amplification, a longer minisatellites sequence etc. is_obsolete: true !{since=beta13} -consider: EDAM_operation:0415 ! Nucleic acid feature detection +consider: EDAM_operation:0415 ! Nucleic acid feature prediction [Term] @@ -5280,6 +5688,51 @@ subset: operations def: "Cut (remove) characters or a region from a molecular sequence." [http://edamontology.org] is_a: EDAM_operation:0231 ! Sequence editing +[Term] +id: EDAM_operation:3192 !{since=1.1} +name: Sequence trimming +namespace: operation +subset: operations +def: "Cut (remove) the end from a molecular sequence." [http://edamontology.org] +is_a: EDAM_operation:0369 ! Sequence cutting + + +[Term] +id: EDAM_operation:3212 !{since=1.1} +name: Primer removal +namespace: operation +subset: operations +def: "Remove forward and/or reverse primers from nucleic acid sequences (typically PCR products)." [http://edamontology.org] +is_a: EDAM_operation:0369 ! Sequence cutting +is_a: EDAM_operation:2511 ! Sequence editing (nucleic acid) + + +[Term] +id: EDAM_operation:3189 !{since=1.1} +name: Trim ends +namespace: operation +subset: operations +def: "Trim sequences (typically from an automated DNA sequencer) to remove misleading ends." [http://edamontology.org] +comment: For example trim polyA tails, introns and primer sequence flanking the sequence of amplified exons, or other unwanted sequence. +is_a: EDAM_operation:3192 ! Sequence trimming + +[Term] +id: EDAM_operation:3190 !{since=1.1} +name: Trim vector +namespace: operation +subset: operations +def: "Trim sequences (typically from an automated DNA sequencer) to remove sequence-specific end regions, typically contamination from vector sequences." [http://edamontology.org] +is_a: EDAM_operation:3192 ! Sequence trimming + +[Term] +id: EDAM_operation:3191 !{since=1.1} +name: Trim to reference +namespace: operation +subset: operations +def: "Trim sequences (typically from an automated DNA sequencer) to remove the sequence ends that extend beyond an assembled reference sequence." [http://edamontology.org] +is_a: EDAM_operation:3192 ! Sequence trimming + + [Term] id: EDAM_operation:0370 @@ -5355,7 +5808,7 @@ subset: operations ! alt_id: EDAM_operation:2450 def: "Find (and possibly render) short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences." [http://edamontology.org] is_a: EDAM_operation:0237 ! Repeat sequence analysis -is_a: EDAM_operation:0415 ! Nucleic acid feature detection +is_a: EDAM_operation:0415 ! Nucleic acid feature prediction relationship: has_output EDAM_data:1299 ! Sequence features (repeats) @@ -5387,7 +5840,7 @@ subset: operations def: "Identify common, conserved (homologous) or synonymous transcriptional regulatory motifs (transcription factor binding sites)." [http://edamontology.org] 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_operation:0438 ! Transcription regulatory element prediction -is_a: EDAM_operation:0415 ! Nucleic acid feature detection +is_a: EDAM_operation:0415 ! Nucleic acid feature prediction relationship: has_output EDAM_data:1315 ! Gene features (TFBS) [Term] @@ -5409,6 +5862,8 @@ namespace: operation subset: operations def: "Find (scan for) known motifs, patterns and regular expressions in molecular sequence(s)." [http://edamontology.org] synonym: "Sequence motif detection" EXACT [http://edamontology.org] +synonym: "Motif detection" EXACT [http://edamontology.org] +synonym: "Motif recognition" EXACT [http://edamontology.org] is_a: EDAM_operation:2404 ! Sequence motif processing is_a: EDAM_operation:0253 ! Feature prediction relationship: has_output EDAM_data:1298 ! Sequence features (motifs) @@ -5447,8 +5902,8 @@ comment: This includes methods to render and visualise the properties of a prote synonym: "Protein property rendering" EXACT [http://edamontology.org] is_a: EDAM_operation:2502 ! Protein data processing is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) -relationship: has_input EDAM_data:0897 ! Protein property ! !{min_cardinality=0} -relationship: has_output EDAM_data:0897 ! Protein property ! !{min_cardinality=0} +relationship: has_input EDAM_data:0897 !{min_cardinality=0} ! Protein property +relationship: has_output EDAM_data:0897 !{min_cardinality=0} ! Protein property relationship: has_topic EDAM_topic:0123 ! Protein properties [Term] @@ -5549,7 +6004,7 @@ def: "Predict antigenicity, allergenicity / immunogenicity, allergic cross-react 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_operation:2492 ! Protein interaction prediction is_a: EDAM_operation:3088 ! Protein property calculation (from sequence) -relationship: has_output EDAM_data:1534 !{min_cardinality=1} ! Peptide immunogenicity +relationship: has_output EDAM_data:1534 !{min_cardinality=1} ! Peptide immunogenicity data relationship: has_topic EDAM_topic:0804 ! Immunoinformatics @@ -5687,8 +6142,8 @@ subset: operations def: "Process (read and / or write) RNA secondary structure data." [http://edamontology.org] is_a: EDAM_operation:2482 ! Secondary structure processing is_a: EDAM_operation:2501 ! Nucleic acid data processing -relationship: has_input EDAM_data:0880 ! RNA secondary structure ! !{min_cardinality=0} -relationship: has_output EDAM_data:0880 ! RNA secondary structure ! !{min_cardinality=0} +relationship: has_input EDAM_data:0880 !{min_cardinality=0} ! RNA secondary structure record +relationship: has_output EDAM_data:0880 !{min_cardinality=0} ! RNA secondary structure record relationship: has_topic EDAM_topic:0097 ! Nucleic acid structure analysis relationship: has_topic EDAM_topic:0697 ! RNA structure and alignment @@ -5701,8 +6156,8 @@ subset: operations def: "Process (read and / or write) nucleic acid tertiary structure data." [http://edamontology.org] is_a: EDAM_operation:2465 ! Structure processing is_a: EDAM_operation:2501 ! Nucleic acid data processing -relationship: has_input EDAM_data:1459 ! Nucleic acid structure ! !{min_cardinality=0} -relationship: has_output EDAM_data:1459 ! Nucleic acid structure ! !{min_cardinality=0} +relationship: has_input EDAM_data:1459 !{min_cardinality=0} ! Nucleic acid structure +relationship: has_output EDAM_data:1459 !{min_cardinality=0} ! Nucleic acid structure relationship: has_topic EDAM_topic:0097 ! Nucleic acid structure analysis @@ -5725,8 +6180,8 @@ subset: operations def: "Predict RNA secondary structure (for example knots, pseudoknots, alternative structures etc)." [http://edamontology.org] comment: Methods might use RNA motifs, predicted intermolecular contacts, or RNA sequence-structure compatibility (inverse RNA folding). is_a: EDAM_operation:2439 ! RNA secondary structure processing -is_a: EDAM_operation:0415 ! Nucleic acid feature detection -relationship: has_output EDAM_data:0880 !{min_cardinality=1} ! RNA secondary structure +is_a: EDAM_operation:0415 ! Nucleic acid feature prediction +relationship: has_output EDAM_data:0880 !{min_cardinality=1} ! RNA secondary structure record relationship: has_topic EDAM_topic:0173 ! Nucleic acid structure prediction [Term] @@ -5846,7 +6301,7 @@ synonym: "sequence_feature" RELATED [SO:0000110] is_a: EDAM_operation:2403 ! Sequence analysis is_a: EDAM_operation:2423 ! Prediction, detection and recognition relationship: has_output EDAM_data:1255 !{min_cardinality=1} ! Feature record -relationship: has_topic EDAM_topic:3072 ! Feature prediction +relationship: has_topic EDAM_topic:3072 ! Sequence feature detection [Term] @@ -5856,9 +6311,9 @@ namespace: operation subset: operations def: "Process (read and / or write) a sequence feature table." [http://edamontology.org] is_a: EDAM_operation:2446 ! Sequence processing -relationship: has_input EDAM_data:1270 ! Sequence feature table ! !{min_cardinality=0} -relationship: has_input EDAM_data:2201 ! Sequence record full ! !{min_cardinality=0} -relationship: has_output EDAM_data:1255 ! Sequence features ! !{min_cardinality=0} +relationship: has_input EDAM_data:1270 !{min_cardinality=0} ! Sequence feature table +relationship: has_input EDAM_data:2201 !{min_cardinality=0} ! Sequence record full +relationship: has_output EDAM_data:1255 !{min_cardinality=0} ! Feature record relationship: has_topic EDAM_topic:0160 ! Sequence sites and features [Term] @@ -5878,20 +6333,22 @@ namespace: operation subset: operations def: "Query the features (in a feature table) of molecular sequence(s)." [http://edamontology.org] is_a: EDAM_operation:2453 ! Feature table processing -relationship: has_input EDAM_data:1270 ! Sequence feature table ! !{min_cardinality=0} -relationship: has_input EDAM_data:2201 ! Sequence record full ! !{min_cardinality=0} -relationship: has_output EDAM_data:1255 ! Sequence features +relationship: has_input EDAM_data:1270 !{min_cardinality=0} ! Sequence feature table +relationship: has_input EDAM_data:2201 !{min_cardinality=0} ! Sequence record full +relationship: has_output EDAM_data:1255 ! Feature record [Term] id: EDAM_operation:0256 -name: Feature table comparison +name: Feature comparison namespace: operation subset: operations def: "Compare the feature tables of two or more molecular sequences." [http://edamontology.org] +synonym: "Feature table comparison" EXACT [http://edamontology.org] +synonym: "Sequence feature comparison" EXACT [http://edamontology.org] is_a: EDAM_operation:2453 ! Feature table processing is_a: EDAM_operation:2424 ! Comparison -relationship: has_input EDAM_data:1270 ! Sequence feature table ! !{min_cardinality=0} -relationship: has_input EDAM_data:2201 ! Sequence record full ! !{min_cardinality=0} +relationship: has_input EDAM_data:1270 !{min_cardinality=0} ! Sequence feature table +relationship: has_input EDAM_data:2201 !{min_cardinality=0} ! Sequence record full @@ -5917,7 +6374,7 @@ subset: operations def: "Predict, recognise and identify positional features in protein sequences such as functional sites or regions and secondary structure." [http://edamontology.org] comment: Methods typically involve scanning for known motifs, patterns and regular expressions. synonym: "Sequence feature detection (protein)" EXACT [http://edamontology.org] -is_a: EDAM_operation:3092 ! Protein feature detection +is_a: EDAM_operation:3092 ! Protein feature prediction ! is_a: EDAM_operation:0253 ! Feature prediction is_a: EDAM_operation:2479 ! Protein sequence analysis @@ -5929,7 +6386,7 @@ name: Protein feature prediction (from structure) namespace: operation subset: operations def: "Predict, recognise and identify positional features in proteins from analysing protein structure." [http://edamontology.org] -is_a: EDAM_operation:3092 ! Protein feature detection +is_a: EDAM_operation:3092 ! Protein feature prediction is_a: EDAM_operation:2406 ! Protein structure analysis @@ -5943,7 +6400,7 @@ subset: operations ! alt_id: EDAM_operation:0382 def: "Predict, recognise and identify functional or other key sites within protein sequences, typically by scanning for known motifs, patterns and regular expressions." [http://edamontology.org] synonym: "name: Sequence motif recognition (protein)" EXACT [http://edamontology.org] -is_a: EDAM_operation:0414 ! Protein feature detection (from sequence) +is_a: EDAM_operation:0414 ! Protein feature prediction (from sequence) is_a: EDAM_operation:0239 ! Sequence motif recognition @@ -6039,7 +6496,7 @@ namespace: operation subset: operations def: "Predict RNA and DNA-binding binding sites in protein sequences." [http://edamontology.org] is_a: EDAM_operation:0419 ! Binding site prediction (from sequence) -relationship: has_output EDAM_data:1326 ! Protein features (binding sites) ! !{min_cardinality=0} +relationship: has_output EDAM_data:1326 !{min_cardinality=0} ! Protein features (binding sites) [Term] id: EDAM_operation:0421 @@ -6096,6 +6553,20 @@ def: "Detect or predict signal peptides (and typically predict subcellular local is_a: EDAM_operation:0418 ! Protein signal peptide detection + + +[Term] +id: EDAM_operation:3222 !{since=1.1} +name: Peak calling +namespace: operation +subset: operations +def: "Identify putative protein-binding regions in a genome sequence from analysis of Chip-sequencing data or ChIP-on-chip data." [http://edamontology.org] +comment: Chip-sequencing combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to generate a set of reads, which are aligned to a genome sequence. The enriched areas contain the binding sites of DNA-associated proteins. For example, a transcription factor binding site. ChIP-on-chip in contrast combines chromatin immunoprecipitation ('ChIP') with microarray ('chip'). +synonym: "Protein binding peak detection" EXACT [http://edamontology.org] +is_a: EDAM_operation:0415 ! Nucleic acid feature prediction + + + [Term] id: EDAM_operation:2454 name: Gene and gene component prediction @@ -6103,11 +6574,13 @@ namespace: operation subset: operations def: "Detect, predict and identify genes or components of genes in DNA sequences." [http://edamontology.org] synonym: "Gene finding" EXACT [http://edamontology.org] -is_a: EDAM_operation:0415 ! Nucleic acid feature detection -relationship: has_output EDAM_data:1300 ! Nucleic acid features (gene structure) +is_a: EDAM_operation:0415 ! Nucleic acid feature prediction +relationship: has_output EDAM_data:1300 ! Nucleic acid features (gene and transcript structure) relationship: has_topic EDAM_topic:0109 ! Gene finding + + [Term] id: EDAM_operation:0425 name: Whole gene prediction @@ -6133,7 +6606,7 @@ name: Transposon prediction namespace: operation subset: operations def: "Detect or predict transposons, retrotransposons / retrotransposition signatures etc." [http://edamontology.org] -is_a: EDAM_operation:0415 ! Nucleic acid feature detection +is_a: EDAM_operation:0415 ! Nucleic acid feature prediction relationship: has_output EDAM_data:1301 ! Nucleic acid features (mobile genetic elements) [Term] @@ -6142,7 +6615,7 @@ name: PolyA signal detection namespace: operation subset: operations def: "Detect polyA signals in nucleotide sequences." [http://edamontology.org] -is_a: EDAM_operation:0415 ! Nucleic acid feature detection +is_a: EDAM_operation:0415 ! Nucleic acid feature prediction relationship: has_output EDAM_data:1302 ! Nucleic acid features (PolyA signal or site) [Term] @@ -6153,7 +6626,7 @@ subset: operations ! alt_id: EDAM_operation:2455 def: "Detect quadruplex-forming motifs in nucleotide sequences." [http://edamontology.org] comment: Quadruplex (4-stranded) structures are formed by guanine-rich regions and are implicated in various important biological processes and as therapeutic targets. -is_a: EDAM_operation:0415 ! Nucleic acid feature detection +is_a: EDAM_operation:0415 ! Nucleic acid feature prediction synonym: "Quadruplex structure prediction" EXACT [http://edamontology.org] relationship: has_output EDAM_data:1303 ! Nucleic acid features (quadruplexes) relationship: has_topic EDAM_topic:0173 ! Nucleic acid structure prediction @@ -6168,7 +6641,7 @@ def: "Find CpG rich regions in a nucleotide sequence or isochores in genome sequ 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. This includes methods that visualise CpG rich regions in a nucleotide sequence, for example plot isochores in a genome sequence. synonym: "CpG island and isochores detection" EXACT [http://edamontology.org] synonym: "CpG island and isochores rendering" EXACT [http://edamontology.org] -is_a: EDAM_operation:0415 ! Nucleic acid feature detection +is_a: EDAM_operation:0415 ! Nucleic acid feature prediction relationship: has_output EDAM_data:1304 ! Nucleic acid features (CpG island and isochore) relationship: has_topic EDAM_topic:0157 ! Sequence composition analysis @@ -6179,7 +6652,7 @@ name: Restriction site recognition namespace: operation subset: operations def: "Find and identify restriction enzyme cleavage sites (restriction sites) in (typically) DNA sequences, for example to generate a restriction map." [http://edamontology.org] -is_a: EDAM_operation:0415 ! Nucleic acid feature detection +is_a: EDAM_operation:0415 ! Nucleic acid feature prediction relationship: has_output EDAM_data:1305 ! Nucleic acid features (restriction sites) relationship: has_topic EDAM_topic:0100 ! Nucleic acid restriction @@ -6190,7 +6663,7 @@ namespace: operation subset: operations def: "Identify, predict or analyse splice sites in nucleotide sequences." [http://edamontology.org] comment: Methods might require a pre-mRNA or genomic DNA sequence. -is_a: EDAM_operation:0415 ! Nucleic acid feature detection +is_a: EDAM_operation:0415 ! Nucleic acid feature prediction relationship: has_output EDAM_data:1307 ! Nucleic acid features (splice sites) relationship: has_topic EDAM_topic:0114 ! Gene structure and RNA splicing @@ -6209,7 +6682,7 @@ name: Nucleosome formation or exclusion sequence prediction namespace: operation subset: operations def: "Identify or predict nucleosome exclusion sequences (nucleosome free regions) in DNA." [http://edamontology.org] -is_a: EDAM_operation:0415 ! Nucleic acid feature detection +is_a: EDAM_operation:0415 ! Nucleic acid feature prediction relationship: has_output EDAM_data:1306 ! Nucleic acid features (nucleosome exclusion sequences) @@ -6258,7 +6731,7 @@ subset: operations def: "Predict selenocysteine insertion sequence (SECIS) in a DNA sequence." [http://edamontology.org] comment: SECIS elements are around 60 nucleotides in length with a stem-loop structure directs the cell to translate UGA codons as selenocysteines. is_a: EDAM_operation:0426 ! Gene component prediction -relationship: has_output EDAM_data:1300 ! Nucleic acid features (gene structure) +relationship: has_output EDAM_data:1300 ! Nucleic acid features (gene and transcript structure) [Term] id: EDAM_operation:0438 @@ -6512,8 +6985,8 @@ subset: operations def: "Process (read and / or write) protein secondary structure data." [http://edamontology.org] is_a: EDAM_operation:2482 ! Secondary structure processing is_a: EDAM_operation:2502 ! Protein data processing -relationship: has_input EDAM_data:0876 ! Protein features (secondary structure) ! !{min_cardinality=0} -relationship: has_output EDAM_data:0876 ! Protein features (secondary structure) ! !{min_cardinality=0} +relationship: has_input EDAM_data:0876 !{min_cardinality=0} ! Protein features (secondary structure) +relationship: has_output EDAM_data:0876 !{min_cardinality=0} ! Protein features (secondary structure) relationship: has_topic EDAM_topic:0694 ! Protein secondary structure [Term] @@ -6536,7 +7009,7 @@ def: "Predict secondary structure of protein sequences." [http://edamontology.or comment: Methods might use amino acid composition, local sequence information, multiple sequence alignments, physicochemical features, estimated energy content, statistical algorithms, hidden Markov models, support vector machines, kernel machines, neural networks etc. synonym: "Secondary structure prediction (protein)" EXACT [http://edamontology.org] is_a: EDAM_operation:2444 ! Protein secondary structure processing -is_a: EDAM_operation:0414 ! Protein feature detection (from sequence) +is_a: EDAM_operation:0414 ! Protein feature prediction (from sequence) is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) relationship: has_output EDAM_data:0876 !{min_cardinality=1} ! Protein features (secondary structure) relationship: has_topic EDAM_topic:0178 ! Protein secondary structure prediction @@ -6558,7 +7031,7 @@ namespace: operation subset: operations def: "Assign secondary structure from protein coordinate data." [http://edamontology.org] is_a: EDAM_operation:0319 ! Protein secondary structure assignment -is_a: EDAM_operation:3090 ! Protein feature detection (from structure) +is_a: EDAM_operation:3090 ! Protein feature prediction (from structure) [Term] id: EDAM_operation:0535 @@ -6740,8 +7213,8 @@ def: "Model the structure of a protein in complex with a small molecule or anoth comment: This includes protein-protein interactions, protein-nucleic acid, protein-ligand binding etc. Methods might predict whether the molecules are likely to bind in vivo, their conformation when bound, the strength of the interaction, possible mutations to achieve bonding and so on. is_a: EDAM_operation:0477 ! Protein modelling is_a: EDAM_operation:2492 ! Protein interaction prediction -relationship: has_output EDAM_data:1461 ! Protein-ligand complex ! !{min_cardinality=0} -relationship: has_output EDAM_data:2877 ! Protein complex ! !{min_cardinality=0} +relationship: has_output EDAM_data:1461 !{min_cardinality=0} ! Protein-ligand complex +relationship: has_output EDAM_data:2877 !{min_cardinality=0} ! Protein complex relationship: has_topic EDAM_topic:0177 ! Molecular docking @@ -6754,7 +7227,7 @@ def: "Align molecular sequence to structure in 3D space (threading)." [http://ed comment: Use this concept 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: "Sequence-structure alignment" EXACT [http://edamontology.org] is_a: EDAM_operation:0303 ! Protein fold recognition -is_a: EDAM_operation:2928 ! Alignment +is_a: EDAM_operation:2928 ! Alignment construction relationship: has_input EDAM_data:1460 !{min_cardinality=1} ! Protein structure relationship: has_output EDAM_data:0893 !{min_cardinality=1} ! Sequence-structure alignment relationship: has_topic EDAM_topic:0175 ! Homology modelling @@ -6850,7 +7323,7 @@ subset: operations def: "Predict the interactions of proteins with other molecules." [http://edamontology.org] is_a: EDAM_operation:2405 ! Protein interaction data processing is_a: EDAM_operation:3023 ! Prediction, detection and recognition (protein) -relationship: has_output EDAM_data:0906 !{min_cardinality=1} ! Protein report (interaction) +relationship: has_output EDAM_data:0906 !{min_cardinality=1} ! Protein interaction [Term] id: EDAM_operation:2464 @@ -6879,7 +7352,7 @@ namespace: operation subset: operations def: "Identify or predict protein-protein interactions, interfaces, binding sites etc in protein structures." [http://edamontology.org] is_a: EDAM_operation:2464 ! Protein-protein interaction prediction -is_a: EDAM_operation:3090 ! Protein feature detection (from structure) +is_a: EDAM_operation:3090 ! Protein feature prediction (from structure) @@ -6891,8 +7364,8 @@ subset: operations def: "Process (read and / or write) a network of protein interactions." [http://edamontology.org] is_a: EDAM_operation:2405 ! Protein interaction data processing is_a: EDAM_operation:2438 ! Pathway or network processing -relationship: has_input EDAM_data:1663 ! Pathway or network (protein-protein interaction) ! !{min_cardinality=0} -relationship: has_output EDAM_data:1663 ! Pathway or network (protein-protein interaction) ! !{min_cardinality=0} +relationship: has_input EDAM_data:1663 !{min_cardinality=0} ! Pathway or network (protein-protein interaction) +relationship: has_output EDAM_data:1663 !{min_cardinality=0} ! Pathway or network (protein-protein interaction) relationship: has_topic EDAM_topic:3044 ! Protein interaction networks [Term] @@ -6930,6 +7403,62 @@ is_a: EDAM_operation:1778 ! Protein function comparison relationship: has_input EDAM_data:1663 !{min_cardinality=2} ! Pathway or network (protein-protein interaction) + +[Term] +id: EDAM_operation:3197 !{since=1.1} +name: Genetic variation analysis +namespace: operation +subset: operations +def: "Analyse a genetic variation, for example to annotate its location, alleles, classification, and effects on individual transcripts predicted for a gene model." [http://edamontology.org] +comment: Genetic variation annotation provides contextual interpretation of coding SNP consequences in transcripts. It allows comparisons to be made between variation data in different populations or strains for the same transcript. +synonym: "Sequence variation analysis" EXACT [http://edamontology.org] +synonym: "Genetic variation annotation" EXACT [http://edamontology.org] +is_a: EDAM_operation:2508 ! Nucleic acid sequence comparison +relationship: has_output EDAM_data:0918 ! Nucleic acid features (variation) + + +[Term] +id: EDAM_operation:3227 !{since=1.1} +name: Variant mapping +namespace: operation +subset: operations +def: "Identify and map genomic alterations, including single nucleotide polymorphisms, short indels and structural variants, in a genome sequence." [http://edamontology.org] +comment: Methods often utilise a database of aligned reads. +synonym: "Variant calling" EXACT [http://edamontology.org] +is_a: EDAM_operation:3197 ! Genetic variation analysis + + +[Term] +id: EDAM_operation:3228 !{since=1.1} +name: Structural variation discovery +namespace: operation +subset: operations +def: "Detect large regions in a genome subject to copy-number variation, or other structural variations in genome(s)." [http://edamontology.org] +comment: Methods might involve analysis of whole-genome array comparative genome hybridization or single-nucleotide polymorphism arrays, paired-end mapping of sequencing data, or from analysis of short reads from new sequencing technologies. +is_a: EDAM_operation:3197 ! Genetic variation analysis + + +[Term] +id: EDAM_operation:3196 !{since=1.1} +name: Genotyping +namespace: operation +subset: operations +def: "Analyse DNA sequence data to identify differences between the genetic composition (genotype) of an individual compared to other individual's or a reference sequence." [http://edamontology.org] +comment: Methods might consider cytogenetic analyses, copy number polymorphism (and calculate copy number calls for copy-number variation(CNV) regions), single nucleotide polymorphism (SNP), , rare copy number variation (CNV) identification, loss of heterozygosity data and so on. +is_a: EDAM_operation:3197 ! Genetic variation analysis + + +! Link frameshift error detection and SNP detection to this one +[Term] +id: EDAM_operation:3202 !{since=1.1} +name: Mutation detection +namespace: operation +subset: operations +def: "Detect mutations in multiple DNA sequences, for example, from the alignment and comparison of the fluorescent traces produced by DNA sequencing hardware." [http://edamontology.org] +synonym: "Polymorphism detection" EXACT [http://edamontology.org] +is_a: EDAM_operation:3197 ! Genetic variation analysis + + [Term] id: EDAM_operation:0484 name: SNP detection @@ -6938,10 +7467,21 @@ subset: operations def: "Find single nucleotide polymorphisms (SNPs) between sequences." [http://edamontology.org] comment: This includes functional SNPs for large-scale genotyping purposes, disease-associated non-synonymous SNPs etc. synonym: "Single nucleotide polymorphism detection" EXACT [http://edamontology.org] -is_a: EDAM_operation:2508 ! Nucleic acid sequence comparison -is_a: EDAM_operation:2508 ! Nucleic acid sequence comparison +is_a: EDAM_operation:3202 ! Mutation detection +is_a: EDAM_operation:0415 ! Nucleic acid feature prediction relationship: has_output EDAM_data:2885 ! Nucleic acid features (polymorphism annotation) + +[Term] +id: EDAM_operation:3201 !{since=1.1} +name: SNP calling +namespace: operation +subset: operations +def: "Identify single nucleotide change in base positions in sequencing data that differ from a reference genome and which might, especially by reference to population frequency or functional data, indicate a polymorphism." [http://edamontology.org] +comment: Operations usually score confidence in the prediction or some other statistical measure of evidence. +is_a: EDAM_operation:0484 ! SNP detection + + [Term] id: EDAM_operation:0485 name: Radiation Hybrid Mapping @@ -6951,6 +7491,19 @@ def: "Generate a physical (radiation hybrid) map of genetic markers in a DNA seq is_a: EDAM_operation:2944 ! Physical mapping relationship: has_output EDAM_data:2870 !{min_cardinality=1} ! Radiation hybrid map + +[Term] +id: EDAM_operation:3186 !{since=1.1} +name: Bisulfite mapping +namespace: operation +subset: operations +def: "The mapping of methylation sites in a DNA (genome) sequence." [http://edamontology.org] +comment: Bisulfite mapping follows high-throughput sequencing of DNA which has undergone bisulfite treatment followed by PCR amplification; unmethylated cytosines are specifically converted to thymine, allowing the methylation status of cytosine in the DNA to be detected. +synonym: "Bisulfite sequence mapping" EXACT [http://edamontology.org] +synonym: "Bisulfite sequence alignment" EXACT [http://edamontology.org] +is_a: EDAM_operation:2944 ! Physical mapping + + [Term] id: EDAM_operation:0486 name: Functional mapping @@ -6968,8 +7521,9 @@ name: Haplotype inference namespace: operation subset: operations def: "Infer haplotypes, either alleles at multiple loci that are transmitted together on the same chromosome, or a set of single nucleotide polymorphisms (SNPs) on a single chromatid that are statistically associated." [http://edamontology.org] -comment: Haplotype inference can help in population genetic studies and the identification of complex disease genes. Tools might use combinatorial functions (for example parsimony) or a likelihood function or model with optimization such as minimum error correction (MEC) model, expectation-maximization algorithm (EM), genetic algorithm or Markov chain Monte Carlo (MCMC). +comment: Haplotype inference can help in population genetic studies and the identification of complex disease genes, , and is typically based on aligned single nucleotide polymorphism (SNP) fragments. Haplotype comparison is a useful way to characterize the genetic variation between individuals. An individual's haplotype describes which nucleotide base occurs at each position for a set of common SNPs. Tools might use combinatorial functions (for example parsimony) or a likelihood function or model with optimization such as minimum error correction (MEC) model, expectation-maximization algorithm (EM), genetic algorithm or Markov chain Monte Carlo (MCMC). synonym: "Haplotype mapping" EXACT [http://edamontology.org] +synonym: "Haplotype reconstruction" EXACT [http://edamontology.org] is_a: EDAM_operation:0283 ! Linkage analysis relationship: has_output EDAM_data:1863 !{min_cardinality=1} ! Haplotype map @@ -6994,10 +7548,10 @@ def: "Process (read and / or write) codon usage data, e.g. analyse codon usage t synonym: "synon: Codon usage table analysis" EXACT [http://edamontology.org] synonym: "synon: Codon usage data analysis" EXACT [http://edamontology.org] is_a: EDAM_operation:2501 ! Nucleic acid data processing -relationship: has_input EDAM_data:2977 ! Nucleic acid sequence ! !{min_cardinality=0} -relationship: has_input EDAM_data:1597 ! Codon usage table ! !{min_cardinality=0} -relationship: has_output EDAM_data:1597 ! Codon usage table ! !{min_cardinality=0} -relationship: has_output EDAM_data:0914 ! Codon usage report ! !{min_cardinality=0} +relationship: has_input EDAM_data:2977 !{min_cardinality=0} ! Nucleic acid sequence +relationship: has_input EDAM_data:1597 !{min_cardinality=0} ! Codon usage table +relationship: has_output EDAM_data:1597 !{min_cardinality=0} ! Codon usage table +relationship: has_output EDAM_data:0914 !{min_cardinality=0} ! Codon usage report relationship: has_topic EDAM_topic:0107 ! Codon usage analysis @@ -7008,8 +7562,8 @@ namespace: operation subset: operations def: "Process (read and / or write) a codon usage table." [http://edamontology.org] is_a: EDAM_operation:0286 ! Codon usage analysis -relationship: has_input EDAM_data:1597 ! Codon usage table ! !{min_cardinality=0} -relationship: has_output EDAM_data:1597 ! Codon usage table ! !{min_cardinality=0} +relationship: has_input EDAM_data:1597 !{min_cardinality=0} ! Codon usage table +relationship: has_output EDAM_data:1597 !{min_cardinality=0} ! Codon usage table [Term] id: EDAM_operation:0287 @@ -7079,6 +7633,63 @@ def: "Compare two or more codon usage tables." [http://edamontology.org] is_a: EDAM_operation:2433 ! Codon usage table processing is_a: EDAM_operation:2998 ! Nucleic acid comparison + +[Term] +id: EDAM_operation:3193 !{since=1.1} +name: Genome comparison +namespace: operation +subset: operations +def: "Compare two (tpyically huge) molecular sequences that represent genomes." [http://edamontology.org] +is_a: EDAM_operation:2451 ! Sequence comparison + +[Term] +id: EDAM_operation:3194 !{since=1.1} +name: Genome feature comparison +namespace: operation +subset: operations +def: "Compare the features of two genome sequences." [http://edamontology.org] +comment: Genomic elements that might be compared include genes, indels, single nucleotide polymorphisms (SNPs), retrotransposons, tandem repeats and so on. +is_a: EDAM_operation:0256 ! Feature comparison + + +[Term] +id: EDAM_operation:3182 !{since=1.1} +name: Genome alignment construction +namespace: operation +subset: operations +def: "Align two or more (tpyically huge) molecular sequences that represent genomes." [http://edamontology.org] +synonym: "Genome alignment" EXACT [http://edamontology.org] +is_a: EDAM_operation:0292 ! Sequence alignment construction + + +[Term] +id: EDAM_operation:3198 !{since=1.1} +name: Oligonucleotide alignment construction +namespace: operation +subset: operations +def: "Align short oligonucleotide sequences (reads) to a larger (genomic) sequence." [http://edamontology.org] +comment: The purpose of read mapping is to identify the location of sequenced fragments within a reference genome and assumes that there is, in fact, at least local similarity between the fragment and reference sequences. +synonym: "Short sequence read mapping" EXACT [http://edamontology.org] +synonym: "Short read mapping" EXACT [http://edamontology.org] +synonym: "Read mapping" EXACT [http://edamontology.org] +synonym: "Short oligonucleotide alignment" EXACT [http://edamontology.org] +synonym: "Oligonucleotide mapping" EXACT [http://edamontology.org] +synonym: "Oligonucleotide alignment" EXACT [http://edamontology.org] +synonym: "Short read alignment" EXACT [http://edamontology.org] +synonym: "Read alignment" EXACT [http://edamontology.org] +is_a: EDAM_operation:0292 ! Sequence alignment construction + + +[Term] +id: EDAM_operation:3199 !{since=1.1} +name: Split read mapping +namespace: operation +subset: operations +def: "A varient of oligonucleotide mapping where a read is mapped to two separate locations because of possible structural variation." [http://edamontology.org] +is_a: EDAM_operation:3198 ! Oligonucleotide alignment construction + + + [Term] id: EDAM_operation:0491 name: Pairwise sequence alignment construction @@ -7223,7 +7834,7 @@ synonym: "RNA secondary structure alignment" EXACT [http://edamontology.org] is_a: EDAM_operation:2439 ! RNA secondary structure processing is_a: EDAM_operation:0500 ! Secondary structure alignment construction synonym: "Secondary structure alignment (RNA)" EXACT [http://edamontology.org] -relationship: has_input EDAM_data:0880 !{min_cardinality=2} ! RNA secondary structure +relationship: has_input EDAM_data:0880 !{min_cardinality=2} ! RNA secondary structure record relationship: has_output EDAM_data:0881 !{min_cardinality=1} ! Secondary structure alignment (RNA) [Term] @@ -7292,7 +7903,7 @@ namespace: operation subset: operations def: "Align protein tertiary structures." [http://edamontology.org] is_obsolete: true !{since=beta13} -consider: EDAM_operation:0295 ! Structure alignment +consider: EDAM_operation:0295 ! Structure alignment construction [Term] id: EDAM_operation:0506 @@ -7301,7 +7912,7 @@ namespace: operation subset: operations def: "Align RNA tertiary structures." [http://edamontology.org] is_obsolete: true !{since=beta13} -consider: EDAM_operation:0295 ! Structure alignment +consider: EDAM_operation:0295 ! Structure alignment construction [Term] id: EDAM_operation:0507 @@ -7467,7 +8078,7 @@ def: "Align molecular sequence(s) to structural (3D) profile(s) or template(s) ( synonym: "Sequence-3D profile alignment" EXACT [http://edamontology.org] comment: Methods might perform one-to-one, one-to-many or many-to-many comparisons. is_a: EDAM_operation:0303 ! Protein fold recognition -is_a: EDAM_operation:2928 ! Alignment +is_a: EDAM_operation:2928 ! Alignment construction is_a: EDAM_operation:2403 ! Sequence analysis relationship: has_input EDAM_data:0889 !{min_cardinality=2} ! Structural (3D) profile relationship: has_output EDAM_data:0891 !{min_cardinality=1} ! Sequence-3D profile alignment @@ -7484,7 +8095,7 @@ comment: Primer design involves predicting or selecting primers that are specifi synonym: "PCR primer prediction" EXACT [http://edamontology.org] is_a: EDAM_operation:2419 ! Primer and probe design relationship: has_input EDAM_data:2977 ! Nucleic acid sequence -relationship: has_output EDAM_data:1240 ! PCR primers ! !{min_cardinality=0} +relationship: has_output EDAM_data:1240 !{min_cardinality=0} ! PCR primers relationship: has_topic EDAM_topic:3032 ! Primer or probe design [Term] @@ -7511,6 +8122,17 @@ def: "Perform in-silico (virtual) PCR." [http://edamontology.org] is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis relationship: has_topic EDAM_topic:0077 ! Nucleic acid analysis + +[Term] +id: EDAM_operation:3187 +name: Sequence contamination filtering +namespace: operation +subset: operations +def: "Identify and filter a (typically large) sequence data set to remove sequences from contaminants in the sample that was sequenced." [http://edamontology.org] +is_a: EDAM_operation:2478 ! Nucleic acid sequence analysis +relationship: has_topic EDAM_topic:0077 ! Nucleic acid analysis + + [Term] id: EDAM_operation:0517 name: PCR primer design (for large scale sequencing) @@ -7518,7 +8140,7 @@ namespace: operation subset: operations def: "Predict primers for large scale sequencing." [http://edamontology.org] is_a: EDAM_operation:0308 ! PCR primer design -relationship: has_topic EDAM_topic:0102 ! Sequencing and mapping +relationship: has_topic EDAM_topic:3168 ! Sequencing [Term] id: EDAM_operation:0518 @@ -7563,6 +8185,16 @@ subset: operations def: "Predict primers for methylation PCRs." [http://edamontology.org] is_a: EDAM_operation:0308 ! PCR primer design + +[Term] +id: EDAM_operation:3183 !{since=1.1} +name: Localized reassembly +namespace: operation +subset: operations +def: "Reconstruction of a sequence assembly in a localised area." [http://edamontology.org] +is_a: EDAM_operation:0310 ! Sequence assembly + + [Term] id: EDAM_operation:0523 name: Sequence assembly (mapping assembly) @@ -7615,10 +8247,10 @@ namespace: operation subset: operations def: "Process (read and / or write) a gene expression profile." [http://edamontology.org] is_a: EDAM_operation:2495 ! Gene expression data processing -relationship: has_input EDAM_data:0928 ! Gene expression profile ! !{min_cardinality=0} -relationship: has_output EDAM_data:0928 ! Gene expression profile ! !{min_cardinality=0} +relationship: has_input EDAM_data:0928 !{min_cardinality=0} ! Gene expression profile +relationship: has_output EDAM_data:0928 !{min_cardinality=0} ! Gene expression profile relationship: has_topic EDAM_topic:0203 ! Transcriptomics -relationship: has_topic EDAM_topic:0200 ! Microarrays + [Term] @@ -7648,9 +8280,8 @@ namespace: operation subset: operations def: "Process (read and / or write) a network of gene regulation." [http://edamontology.org] is_a: EDAM_operation:2438 ! Pathway or network processing -relationship: has_input EDAM_data:2961 ! Pathway or network (gene regulation) ! !{min_cardinality=0} -relationship: has_output EDAM_data:2961 ! Pathway or network (gene regulation) ! !{min_cardinality=0} -relationship: has_topic EDAM_topic:0197 ! Gene expression resources +relationship: has_input EDAM_data:2961 !{min_cardinality=0} ! Pathway or network (gene regulation) +relationship: has_output EDAM_data:2961 !{min_cardinality=0} ! Pathway or network (gene regulation) relationship: has_topic EDAM_topic:2846 ! Gene regulatory networks @@ -7704,7 +8335,7 @@ name: Splice transcript prediction namespace: operation subset: operations def: "Predict splicing alternatives or transcript isoforms from analysis of sequence data." [http://edamontology.org] -is_a: EDAM_operation:2499 ! Splicing modelling +is_a: EDAM_operation:2499 ! Splicing analysis relationship: has_topic EDAM_topic:0114 ! Gene structure and RNA splicing [Term] @@ -7730,11 +8361,34 @@ is_a: EDAM_operation:0315 ! Gene expression profile comparison relationship: has_output EDAM_data:3111 ! Processed microarray data [Term] +id: EDAM_operation:3223 !{since=1.1} +name: Differential expression analysis +namespace: operation +subset: operations +def: "Identify (typically from analysis of microarray or RNA-seq data) genes whose expression levels are significantly different between two sample groups." [http://edamontology.org] +comment: Differential expression analysis is used, for example, to identify which genes are up-regulated (increased expression) or down-regulated (decreased expression) between a group treated with a drug and a control groups. +synonym: "Differentially expressed gene identification" EXACT [http://edamontology.org] +is_a: EDAM_operation:0315 ! Gene expression profile comparison + + +[Term] +id: EDAM_operation:3224 !{since=1.1} +name: Gene set testing +namespace: operation +subset: operations +def: "Analyse gene expression patterns (typically from DNA microarray datasets) to identify sets of genes that are associated with a specific trait, condition, clinical outcome etc." [http://edamontology.org] +comment: Gene sets can be defined beforehand by biological function, chromosome locations and so on. +is_a: EDAM_operation:2435 ! Gene expression profile processing + + +[Term] id: EDAM_operation:0314 name: Gene expression profile generation namespace: operation subset: operations def: "Generate a gene expression profile or pattern, for example from microarray data." [http://edamontology.org] +synonym: "Expression profiling" EXACT [http://edamontology.org] +synonym: "Gene expression profiling" EXACT [http://edamontology.org] is_a: EDAM_operation:2435 ! Gene expression profile processing relationship: has_output EDAM_data:0928 !{min_cardinality=1} ! Gene expression profile @@ -7782,6 +8436,19 @@ relationship: has_output EDAM_data:2984 ! Pathway or network report [Term] +id: EDAM_operation:3232 !{since=1.1} +name: Gene expression QTL analysis +namespace: operation +subset: operations +def: "Combine classical quantitative trait loci (QTL) analysis with gene expression profiling, for example, to describe describe cis- and trans-controlling elements for the expression of phenotype associated genes." [http://edamontology.org] +synonym: "eQTL profiling" EXACT [http://edamontology.org] +synonym: "expression QTL profiling" EXACT [http://edamontology.org] +synonym: "expression quantitative trait loci profiling" EXACT [http://edamontology.org] +is_a: EDAM_operation:0532 ! Gene expression profile analysis +relationship: has_output EDAM_data:2984 ! Pathway or network report + + +[Term] id: EDAM_operation:0527 name: Tag mapping namespace: operation @@ -7790,7 +8457,7 @@ def: "Make gene to tag assignments (tag mapping) of SAGE, MPSS and SBS data, by comment: Tag mapping might assign experimentally obtained tags to known transcripts or annotate potential virtual tags in a genome. synonym: "Tag to gene assignment" EXACT [http://edamontology.org] is_a: EDAM_operation:2436 ! Gene expression profile annotation -relationship: has_output EDAM_data:0936 ! Sequence tag profile (with gene assignment) ! !{min_cardinality=0} +relationship: has_output EDAM_data:0936 !{min_cardinality=0} ! Sequence tag profile (with gene assignment) [Term] id: EDAM_operation:0528 @@ -7941,8 +8608,8 @@ subset: operations def: "Process (read and / or write) a protein tertiary structure." [http://edamontology.org] is_a: EDAM_operation:2465 ! Structure processing is_a: EDAM_operation:2502 ! Protein data processing -relationship: has_input EDAM_data:1460 ! Protein structure ! !{min_cardinality=0} -relationship: has_output EDAM_data:1460 ! Protein structure ! !{min_cardinality=0} +relationship: has_input EDAM_data:1460 !{min_cardinality=0} ! Protein structure +relationship: has_output EDAM_data:1460 !{min_cardinality=0} ! Protein structure relationship: has_topic EDAM_topic:0698 ! Protein tertiary structure @@ -7957,7 +8624,7 @@ comment: This might be a residue-level search for properties such as solvent acc is_a: EDAM_operation:2406 ! Protein structure analysis is_a: EDAM_operation:0250 ! Protein property calculation synonym: "Protein structural property calculation" EXACT [http://edamontology.org] -relationship: has_output EDAM_data:0897 ! Protein property ! !{min_cardinality=0} +relationship: has_output EDAM_data:0897 !{min_cardinality=0} ! Protein property relationship: has_topic EDAM_topic:0123 ! Protein properties relationship: has_topic EDAM_topic:2814 ! Protein structure analysis @@ -7981,7 +8648,7 @@ subset: operations def: "Identify or screen for 3D structural motifs in protein structure(s)." [http://edamontology.org] 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 [http://edamontology.org] -is_a: EDAM_operation:3090 ! Protein feature detection (from structure) +is_a: EDAM_operation:3090 ! Protein feature prediction (from structure) relationship: has_output EDAM_data:0899 !{min_cardinality=1} ! Protein features (3D motif) relationship: has_topic EDAM_topic:0166 ! Protein structural motifs and surfaces @@ -7991,7 +8658,7 @@ name: Protein domain recognition namespace: operation subset: operations def: "Identify structural domains in a protein structure from first principles (for example calculations on structural compactness)." [http://edamontology.org] -is_a: EDAM_operation:3090 ! Protein feature detection (from structure) +is_a: EDAM_operation:3090 ! Protein feature prediction (from structure) relationship: has_output EDAM_data:0901 !{min_cardinality=1} ! Protein features (domains) relationship: has_topic EDAM_topic:0736 ! Protein domains and folds @@ -8352,8 +9019,8 @@ subset: operations def: "Identify or predict catalytic residues, active sites or other ligand-binding sites in protein sequences or structures." [http://edamontology.org] synonym: "Ligand-binding and active site prediction" EXACT [http://edamontology.org] is_a: EDAM_operation:2492 ! Protein interaction prediction -relationship: has_output EDAM_data:1325 ! Protein features (active sites) ! !{min_cardinality=0} -relationship: has_output EDAM_data:1326 ! Protein features (binding sites) ! !{min_cardinality=0} +relationship: has_output EDAM_data:1325 !{min_cardinality=0} ! Protein features (active sites) +relationship: has_output EDAM_data:1326 !{min_cardinality=0} ! Protein features (binding sites) relationship: has_topic EDAM_topic:0148 ! Protein-ligand interactions [Term] @@ -8506,7 +9173,7 @@ def: "Calculate protein residue contacts with nucleic acids in a structure." [ht xref: WHATIF:HasNucleicContacts xref: WHATIF:ShowProteiNucleicContacts is_a: EDAM_operation:2950 ! Residue contact calculation -is_a: EDAM_operation:0389 ! Protein-nucleic acid binding site data analysis +is_a: EDAM_operation:0389 ! Protein-nucleic acid binding site analysis is_a: EDAM_operation:0245 ! Protein structural motif recognition @@ -8679,8 +9346,8 @@ namespace: operation subset: operations def: "Process (read and / or write) a phylogenetic tree." [http://edamontology.org] is_a: EDAM_operation:2420 ! Analysis and processing -relationship: has_input EDAM_data:0872 ! Phylogenetic tree ! !{min_cardinality=0} -relationship: has_output EDAM_data:0872 ! Phylogenetic tree ! !{min_cardinality=0} +relationship: has_input EDAM_data:0872 !{min_cardinality=0} ! Phylogenetic tree +relationship: has_output EDAM_data:0872 !{min_cardinality=0} ! Phylogenetic tree relationship: has_topic EDAM_topic:0084 ! Phylogenetics @@ -8820,7 +9487,7 @@ subset: operations def: "Phylogenetic tree construction from gene frequency data." [http://edamontology.org] is_a: EDAM_operation:0538 ! Phylogenetic tree construction (data centric) relationship: has_input EDAM_data:2873 !{min_cardinality=1} ! Phylogenetic gene frequencies data -relationship: has_topic EDAM_topic:0197 ! Gene expression resources +relationship: has_topic EDAM_topic:0203 ! Transcriptomics [Term] @@ -8930,7 +9597,7 @@ name: Phylogenetic tree annotation namespace: operation subset: operations def: "Annotate a phylogenetic tree with terms from a controlled vocabulary." [http://edamontology.org] -synonym "CDAOAnnotattion" RELATED [http://www.evolutionaryontology.org/cdao.owl#CDAOAnnotation] +synonym: "CDAOAnnotattion" RELATED [http://www.evolutionaryontology.org/cdao.owl#CDAOAnnotation] is_a: EDAM_operation:0326 ! Phylogenetic tree editing is_a: EDAM_operation:0226 ! Annotation @@ -9014,7 +9681,7 @@ namespace: operation subset: operations def: "Reformat (a file or other report of) molecular sequence alignment(s)." [http://edamontology.org] is_a: EDAM_operation:0335 ! File reformatting -is_a: EDAM_operation:2122 ! Sequence alignment editing +is_a: EDAM_operation:2122 ! Sequence alignment file processing [Term] id: EDAM_operation:0563 @@ -9063,6 +9730,19 @@ relationship: has_topic EDAM_topic:0640 ! Nucleic acid sequence analysis [Term] +id: EDAM_operation:3208 !{since=1.1} +name: Genome rendering +namespace: operation +subset: operations +def: "Visualise, format or render a nucleic acid sequence that is part of (and in context of) a complete genome sequence." [http://edamontology.org] +synonym: "Genome browsing" EXACT [http://edamontology.org] +synonym: "Genome viewing" EXACT [http://edamontology.org] +synonym: "Genome visualisation" EXACT [http://edamontology.org] +synonym: "Genome visualization" EXACT [http://edamontology.org] +is_a: EDAM_operation:2515 ! Sequence rendering (nucleic acid) + + +[Term] id: EDAM_operation:2516 name: Sequence rendering (protein) namespace: operation @@ -9083,6 +9763,8 @@ is_a: EDAM_operation:2463 ! Sequence alignment processing relationship: has_input EDAM_data:0863 !{min_cardinality=1} ! Sequence alignment relationship: has_output EDAM_data:1711 !{min_cardinality=1} ! Sequence alignment image + + [Term] id: EDAM_operation:2452 name: Sequence cluster processing @@ -9090,8 +9772,8 @@ namespace: operation subset: operations def: "Process (read and / or write) a sequence cluster." [http://edamontology.org] is_a: EDAM_operation:2420 ! Analysis and processing -relationship: has_input EDAM_data:1235 ! Sequence cluster ! !{min_cardinality=0} -relationship: has_output EDAM_data:1235 ! Sequence cluster ! !{min_cardinality=0} +relationship: has_input EDAM_data:1235 !{min_cardinality=0} ! Sequence cluster +relationship: has_output EDAM_data:1235 !{min_cardinality=0} ! Sequence cluster relationship: has_topic EDAM_topic:0164 ! Sequence clustering @@ -9124,7 +9806,7 @@ subset: operations def: "Visualise RNA secondary structure, knots, pseudoknots etc." [http://edamontology.org] is_a: EDAM_operation:0337 ! Plotting and rendering is_a: EDAM_operation:2439 ! RNA secondary structure processing -relationship: has_input EDAM_data:0880 !{min_cardinality=1} ! RNA secondary structure +relationship: has_input EDAM_data:0880 !{min_cardinality=1} ! RNA secondary structure record [Term] id: EDAM_operation:0569 @@ -9172,8 +9854,8 @@ namespace: operation subset: operations def: "Process (read and / or write) a molecular secondary structure." [http://edamontology.org] is_a: EDAM_operation:2420 ! Analysis and processing -relationship: has_input EDAM_data:2081 ! Secondary structure ! !{min_cardinality=0} -relationship: has_output EDAM_data:2081 ! Secondary structure ! !{min_cardinality=0} +relationship: has_input EDAM_data:2081 !{min_cardinality=0} ! Secondary structure +relationship: has_output EDAM_data:2081 !{min_cardinality=0} ! Secondary structure relationship: has_topic EDAM_topic:0081 ! Structure analysis @@ -9185,8 +9867,8 @@ subset: operations ! alt_id: EDAM_operation:2484 def: "Process (read and / or write) a molecular tertiary structure." [http://edamontology.org] is_a: EDAM_operation:2420 ! Analysis and processing -relationship: has_input EDAM_data:0883 ! Structure ! !{min_cardinality=0} -relationship: has_output EDAM_data:0883 ! Structure ! !{min_cardinality=0} +relationship: has_input EDAM_data:0883 !{min_cardinality=0} ! Structure +relationship: has_output EDAM_data:0883 !{min_cardinality=0} ! Structure relationship: has_topic EDAM_topic:0081 ! Structure analysis [Term] @@ -9209,7 +9891,7 @@ subset: operations def: "Visualise microarray data." [http://edamontology.org] is_a: EDAM_operation:0337 ! Plotting and rendering is_a: EDAM_operation:2435 ! Gene expression profile processing -relationship: has_input EDAM_data:3117 !{min_cardinality=1} ! Microarray hybridisation data +relationship: has_input EDAM_data:3117 !{min_cardinality=1} ! Microarray hybridisation data relationship: has_output EDAM_data:2967 !{min_cardinality=1} ! Microarray image [Term] @@ -9233,6 +9915,19 @@ is_a: EDAM_operation:2515 ! Sequence rendering (nucleic acid) is_a: EDAM_operation:2521 ! Map data processing relationship: has_input EDAM_data:1274 !{min_cardinality=1} ! Map + +[Term] +id: EDAM_operation:3184 !{since=1.1} +name: Sequence assembly rendering +namespace: operation +subset: operations +def: "Render and visualise a DNA sequence assembly." [http://edamontology.org] +synonym: "Assembly rendering" EXACT [http://edamontology.org] +synonym: "Assembly visualisation" EXACT [http://edamontology.org] +synonym: "Sequence assembly visualisation" EXACT [http://edamontology.org] +is_a: EDAM_operation:2515 ! Sequence rendering (nucleic acid) + + [Term] id: EDAM_operation:0574 name: Sequence motif rendering @@ -9631,7 +10326,7 @@ namespace: data subset: data def: "A map of (typically one) DNA sequence annotated with positional or non-positional features." [http://edamontology.org] synonym: "DNA map" EXACT [http://edamontology.org] -relationship: has_topic EDAM_topic:0102 ! Sequencing and mapping +relationship: has_topic EDAM_topic:0102 ! Mapping is_a: EDAM_data:3031 ! Core data [Term] @@ -9652,7 +10347,7 @@ namespace: data subset: data def: "An attribute of a molecular map (genetic or physical)." [http://edamontology.org] is_a: EDAM_data:2337 ! Metadata -relationship: has_topic EDAM_topic:0102 ! Sequencing and mapping +relationship: has_topic EDAM_topic:0102 ! Mapping [Term] @@ -9803,6 +10498,16 @@ comment: This is a broad data type and is used a placeholder for other, more spe is_a: EDAM_data:2083 ! Alignment report + +[Term] +id: EDAM_data:3181 !{since=1.1} +name: Sequence assembly report +namespace: data +subset: data +def: "An informative report about a DNA sequence assembly." [http://edamontology.org] +is_a: EDAM_data:2955 ! Sequence report + + [Term] id: EDAM_data:2598 name: Secondary structure alignment metadata @@ -9887,7 +10592,7 @@ namespace: data subset: data def: "Data from which a phylogenetic tree may be generated." [http://edamontology.org] is_a: EDAM_data:2523 ! Phylogenetic raw data -synonym "Character" RELATED [http://www.evolutionaryontology.org/cdao.owl#Character] +synonym: "Character" RELATED [http://www.evolutionaryontology.org/cdao.owl#Character] ! Phylogenetic character data! Also molecular sequences, microsatellites), polymorphisms (RAPDs, RFLPs, or AFLPs), restriction sites and fragments [Term] @@ -9897,7 +10602,7 @@ namespace: data subset: data def: "The raw data (not just an image) from which a phylogenetic tree is directly generated or plotted, such as topology, lengths (in time or in expected amounts of variance) and a confidence interval for each length." [http://edamontology.org] comment: A phylogenetic tree is usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. See also 'Phylogenetic tree image'. -synonym "Tree" RELATED [http://www.evolutionaryontology.org/cdao.owl#Tree] +synonym: "Tree" RELATED [http://www.evolutionaryontology.org/cdao.owl#Tree] xref: Moby:Tree xref: Moby:phylogenetic_tree xref: Moby:myTree @@ -9914,7 +10619,6 @@ subset: data def: "A report of data concerning or derived from a phylogenetic tree, or from comparing two or more phylogenetic trees." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. synonym: "Phylogenetic tree-derived report" EXACT [http://edamontology.org] -synonym "Tree" RELATED [http://www.evolutionaryontology.org/cdao.owl#Tree] is_a: EDAM_data:2048 ! Report @@ -9937,7 +10641,7 @@ subset: data def: "Data concerning molecular structural data." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. is_obsolete: true !{since=beta13} -consider: EDAM_data:0883 ! Structure data +consider: EDAM_data:0883 ! Structure consider: EDAM_data:2085 ! Structure report @@ -10409,7 +11113,7 @@ synonym: "Gene expression report" EXACT [http://edamontology.org] synonym: "Gene annotation (expression)" EXACT [http://edamontology.org] is_a: EDAM_data:3117 ! Microarray hybridisation data is_a: EDAM_data:0928 ! Gene expression profile -relationship: has_topic EDAM_topic:0197 ! Gene expression resources +relationship: has_topic EDAM_topic:0200 ! Microarrays [Term] @@ -10419,7 +11123,7 @@ namespace: data subset: data def: "Data concerning the hybridisations measured during a microarray experiment." [http://edamontology.org] is_a: EDAM_data:2603 ! Microarray data -relationship: has_topic EDAM_topic:0197 ! Gene expression resources +relationship: has_topic EDAM_topic:0200 ! Microarrays [Term] id: EDAM_data:3112 !{since=beta13} @@ -10576,6 +11280,18 @@ is_a: EDAM_data:2531 ! Experiment annotation [Term] +id: EDAM_data:3231 !{since=1.1} +name: Experiment annotation (GWAS) +namespace: data +subset: data +def: "Metadata on a genome-wide association study (GWAS)." [http://edamontology.org] +synonym: "Experiment annotation (genome-wide association study)" EXACT [http://edamontology.org] +is_a: EDAM_data:2531 ! Experiment annotation + + + + +[Term] id: EDAM_data:0925 name: Sequence assembly namespace: data @@ -10780,6 +11496,17 @@ relationship: has_topic EDAM_topic:0220 ! Data processing and validation [Term] +id: EDAM_data:3210 !{since=1.1} +name: Genome index +namespace: data +subset: data +def: "An index of a genome sequence." [http://edamontology.org] +comment: Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment. +is_a: EDAM_data:0955 ! Data index + + + +[Term] id: EDAM_data:0956 name: Data index report namespace: data @@ -10832,7 +11559,6 @@ subset: data def: "An informative report on a specific chemical compound." [http://edamontology.org] synonym: "Chemical compound annotation" EXACT [http://edamontology.org] synonym: "Small molecule report" EXACT [http://edamontology.org] -synonym: "molecular entity" RELATED [CHEBI:23367] is_a: EDAM_data:2085 ! Structure report is_a: EDAM_data:2529 ! Molecule report relationship: has_topic EDAM_topic:0154 ! Small molecules @@ -10955,7 +11681,7 @@ namespace: data subset: data def: "A body of scientific text, typically a full text article from a scientific journal." [http://edamontology.org] is_a: EDAM_data:3031 ! Core data -relationship: has_topic EDAM_topic:3068 ! Literature data resources +relationship: has_topic EDAM_topic:3068 ! Literature and reference [Term] id: EDAM_data:2857 @@ -10965,7 +11691,7 @@ subset: data def: "Bibliographic data concerning scientific article(s)." [http://edamontology.org] is_a: EDAM_data:2954 ! Article report is_a: EDAM_data:2337 ! Metadata -relationship: has_topic EDAM_topic:3068 ! Literature data resources +relationship: has_topic EDAM_topic:3068 ! Literature and reference [Term] @@ -11651,7 +12377,7 @@ def: "The type of a sequence feature, typically a term or accession from the Seq comment: A feature key indicates the biological nature of the feature or information about changes to or versions of the sequence. synonym: "Sequence feature type" EXACT [http://edamontology.org] synonym: "Sequence feature method" EXACT [http://edamontology.org] -is_a: EDAM_data:2914 ! Sequence feature metadata +is_a: EDAM_data:2914 ! Sequence features metadata [Term] @@ -11661,7 +12387,7 @@ namespace: data subset: data def: "Typically one of the EMBL or Swiss-Prot feature qualifiers." [http://edamontology.org] comment: Feature qualifiers hold information about a feature beyond that provided by the feature key and location. -is_a: EDAM_data:2914 ! Sequence feature metadata +is_a: EDAM_data:2914 ! Sequence features metadata [Term] id: EDAM_data:1022 @@ -11671,7 +12397,7 @@ subset: data def: "Typically an EMBL or Swiss-Prot feature label." [http://edamontology.org] comment: A feature label identifies a feature of a sequence database entry. When used with the database name and the entry's primary accession number, it is a unique identifier of that feature. synonym: "Sequence feature name" EXACT [http://edamontology.org] -is_a: EDAM_data:2914 ! Sequence feature metadata +is_a: EDAM_data:2914 ! Sequence features metadata [Term] id: EDAM_data:1278 @@ -11801,7 +12527,7 @@ def: "A feature which may mapped (positioned) on a genetic or other type of map. comment: Mappable features may be based on Gramene's notion of map features; see http://www.gramene.org/db/cmap/feature_type_info. xref: Moby:MapFeature is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1255 ! Sequence features +consider: EDAM_data:1255 ! Feature record consider: EDAM_data:2019 ! Map attribute consider: EDAM_data:1276 ! Nucleic acid features @@ -11990,7 +12716,7 @@ synonym: "Genome track" EXACT [http://edamontology.org] synonym: "Genomic track" EXACT [http://edamontology.org] synonym: "Genome-browser track" EXACT [http://edamontology.org] synonym: "Genome annotation track" EXACT [http://edamontology.org] -is_a: EDAM_data:1255 ! Sequence features +is_a: EDAM_data:1255 ! Feature record [Term] @@ -12000,7 +12726,7 @@ namespace: data subset: data def: "Annotation of positional sequence features, organized into a standard feature table." [http://edamontology.org] synonym: "Feature table" EXACT [http://edamontology.org] -is_a: EDAM_data:1255 ! Sequence feature annotation +is_a: EDAM_data:1255 ! Feature record [Term] @@ -12014,7 +12740,7 @@ comment: This includes nucleotide sequence feature annotation in any known seque synonym: "Nucleic acid feature table" EXACT [http://edamontology.org] synonym: "Feature table (nucleic acid)" EXACT [http://edamontology.org] is_a: EDAM_data:2084 ! Nucleic acid report -is_a: EDAM_data:1255 ! Sequence features +is_a: EDAM_data:1255 ! Feature record [Term] @@ -12117,7 +12843,7 @@ namespace: data subset: data def: "Features concerning RNA or regions of DNA that encode an RNA molecule." [http://edamontology.org] synonym: "RNA features" EXACT [http://edamontology.org] -is_a: EDAM_data:1300 ! Nucleic acid features (gene structure) +is_a: EDAM_data:1300 ! Nucleic acid features (gene and transcript structure) [Term] id: EDAM_data:3134 !{since=beta13} @@ -12160,7 +12886,7 @@ def: "Protein sequence-specific feature annotation (positional features of a pro comment: This includes protein sequence feature annotation in any known sequence feature table format and any other report of protein features. synonym: "Feature table (protein)" EXACT [http://edamontology.org] synonym: "Protein feature table" EXACT [http://edamontology.org] -is_a: EDAM_data:1255 ! Sequence features +is_a: EDAM_data:1255 ! Feature record is_a: EDAM_data:0896 ! Protein report @@ -12172,7 +12898,7 @@ subset: data def: "Comparative data on sequence features such as statistics, intersections (and data on intersections), differences etc." [http://edamontology.org] comment: This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. is_obsolete: true !{since=beta13} -consider: EDAM_data:1255 ! Sequence features +consider: EDAM_data:1255 ! Feature record [Term] @@ -12182,7 +12908,7 @@ namespace: data subset: data def: "Report on the location of matches to profiles, motifs (conserved or functional patterns) or other signatures in one or more sequences." [http://edamontology.org] comment: Use this concept if another, more specific concept is not available. -is_a: EDAM_data:1255 ! Sequence features +is_a: EDAM_data:1255 ! Feature record [Term] id: EDAM_data:3130 !{since=beta13} @@ -12251,7 +12977,7 @@ subset: data def: "Location of short repetitive subsequences (repeat sequences) in (typically nucleotide) sequences." [http://edamontology.org] comment: The report might include derived data map such as classification, annotation, organization, periodicity etc. synonym: "Repeat sequence map" EXACT [http://edamontology.org] -is_a: EDAM_data:1255 ! Sequence features +is_a: EDAM_data:1255 ! Feature record [Term] @@ -12351,7 +13077,7 @@ name: Nucleic acid features (immunoglobulin gene structure) namespace: data subset: data def: "A report on predicted or actual immunoglobulin gene structure including constant, switch and variable regions and diversity, joining and variable segments." [http://edamontology.org] -is_a: EDAM_data:1300 ! Nucleic acid features (gene structure) +is_a: EDAM_data:1300 ! Nucleic acid features (gene and transcript structure) @@ -12494,7 +13220,7 @@ subset: data def: "A report on operons (operators, promoters and genes) from a bacterial genome." [http://edamontology.org] comment: The report for a query sequence or gene might include the predicted operon leader and trailer gene, gene composition of the operon and associated information, as well as information on the query. synonym: "Gene features (operon)" EXACT [http://edamontology.org] -is_a: EDAM_data:1300 ! Nucleic acid features (gene structure) +is_a: EDAM_data:1300 ! Nucleic acid features (gene and transcript structure) [Term] id: EDAM_data:1312 @@ -12524,7 +13250,7 @@ namespace: data subset: data def: "A report on selenocysteine insertion sequence (SECIS) element in a DNA sequence." [http://edamontology.org] is_obsolete: true !{since=beta13} -consider: EDAM_data:1300 ! Nucleic acid features (gene structure) +consider: EDAM_data:1300 ! Nucleic acid features (gene and transcript structure) [Term] @@ -12621,9 +13347,7 @@ subset: data def: "A report on post-translation modifications in a protein sequence, typically describing the specific sites involved." [http://edamontology.org] synonym: "Protein features (post-translation modification sites)" EXACT [http://edamontology.org] synonym: "Post-translation modification" EXACT [http://edamontology.org] -synonym: "protein modification" RELATED [MOD:00000] -synonym: "protein modification process" RELATED [GO:0006464] -is_a: EDAM_data:1277 ! Protein features +is_a: EDAM_data:2191 ! Protein features (chemical modification) [Term] id: EDAM_data:1325 @@ -13025,7 +13749,7 @@ subset: data def: "Alignment (superimposition) of molecular tertiary (3D) structures." [http://edamontology.org] comment: A tertiary structure alignment will include the untransformed coordinates of one macromolecule, followed by the second (or subsequent) structure(s) with all the coordinates transformed (by rotation / translation) to give a superposition. is_a: EDAM_data:1916 ! Alignment -is_a: EDAM_data:0883 ! Structure data +is_a: EDAM_data:0883 ! Structure relationship: has_topic EDAM_topic:0183 ! Structure alignment [Term] @@ -13635,10 +14359,11 @@ is_a: EDAM_data:1537 ! Protein structure report [Term] id: EDAM_data:0883 -name: Structure data +name: Structure namespace: data subset: data def: "3D coordinate and associated data for a macromolecular tertiary (3D) structure or part of a structure." [http://edamontology.org] +synonym: "Structure data" EXACT [http://edamontology.org] comment: The coordinate data may be predicted or real. relationship: has_topic EDAM_topic:0081 ! Structure analysis is_a: EDAM_data:3031 ! Core data @@ -13727,7 +14452,7 @@ subset: data def: "An informative report of secondary structure (predicted or real) of an RNA molecule." [http://edamontology.org] comment: This includes thermodynamically stable or evolutionarily conserved structures such as knots, pseudoknots etc. xref: Moby:RNAStructML -is_a: EDAM_data:2081 ! Secondary structure record +is_a: EDAM_data:2081 ! Secondary structure relationship: has_topic EDAM_topic:0697 ! RNA structure and alignment @@ -14571,7 +15296,7 @@ subset: data def: "Data on protein-protein interaction(s)." [http://edamontology.org] comment: For example, an informative report about a specific protein complex (of multiple polypeptide chains). synonym: "Protein structure report (protein complex)" EXACT [http://edamontology.org] -is_a: EDAM_data:0906 ! Protein report (interaction) +is_a: EDAM_data:0906 ! Protein interaction relationship: has_topic EDAM_topic:0147 ! Protein-protein interactions @@ -14581,7 +15306,7 @@ name: Protein-ligand interaction namespace: data subset: data def: "Data on protein-ligand (small molecule) interaction(s)." [http://edamontology.org] -is_a: EDAM_data:0906 ! Protein report (interaction) +is_a: EDAM_data:0906 ! Protein interaction relationship: has_topic EDAM_topic:0148 ! Protein-ligand interactions [Term] @@ -14590,7 +15315,7 @@ name: Protein-nucleic acid interaction namespace: data subset: data def: "Data on protein-DNA/RNA interaction(s)." [http://edamontology.org] -is_a: EDAM_data:0906 ! Protein report (interaction) +is_a: EDAM_data:0906 ! Protein interaction relationship: has_topic EDAM_topic:0149 ! Protein-nucleic acid interactions @@ -14627,7 +15352,7 @@ name: Protein-drug interaction namespace: data subset: data def: "Informative report on protein-drug interaction(s) including binding affinity data." [http://edamontology.org] -is_a: EDAM_data:1566 ! Protein ligand interaction +is_a: EDAM_data:1566 ! Protein-ligand interaction [Term] id: EDAM_data:2358 @@ -15021,7 +15746,7 @@ namespace: data subset: data def: "A report on a chromosome aberration such as abnormalities in chromosome structure." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:0919 ! Nucleic acid features (chromosome) +consider: EDAM_data:0919 ! Gene annotation (chromosome) [Term] @@ -15031,7 +15756,7 @@ namespace: data subset: data def: "Data on the influence of genotype on drug response." [http://edamontology.org] comment: The report might correlate gene expression or single-nucleotide polymorphisms with drug efficacy or toxicity. -is_a: EDAM_data:0920 ! Genotype and phenotype annotation +is_a: EDAM_data:0920 ! Genotype/phenotype annotation [Term] @@ -15144,7 +15869,7 @@ id: EDAM_data:0924 name: Sequence trace namespace: data subset: data -def: "A molecular sequence (reads) with associated sequencing metadata (such as base-call quality scores or raw sequencing data)." [http://edamontology.org] +def: "Fluorescence trace data generated by an automated DNA sequencer, which can be interprted as a molecular sequence (reads), given associated sequencing metadata such as base-call quality scores." [http://edamontology.org] comment: This is the raw data produced by a DNA sequencing machine. is_a: EDAM_data:3108 ! Experimental measurement is_a: EDAM_data:2887 ! Sequence record (nucleic acid) @@ -15287,7 +16012,7 @@ def: "Information on a microarray experiment such as conditions, protocol, sampl comment: This might specify which raw data file relates to which sample and information on hybridisations, e.g. which are technical and which are biological replicates. synonym: "Experimental design annotation" EXACT [http://edamontology.org] is_a: EDAM_data:2531 ! Experiment annotation -relationship: has_topic EDAM_topic:0197 ! Gene expression resources +relationship: has_topic EDAM_topic:0200 ! Microarrays [Term] id: EDAM_data:2866 @@ -15465,7 +16190,7 @@ subset: data def: "How the annotation of a sequence feature (for example in EMBL or Swiss-Prot) was derived." [http://edamontology.org] comment: This might be the name and version of a software tool, the name of a database, or 'curated' to indicate a manual annotation (made by a human). is_a: EDAM_data:2042 ! Evidence -is_a: EDAM_data:2914 ! Sequence feature metadata +is_a: EDAM_data:2914 ! Sequence features metadata [Term] @@ -15672,7 +16397,7 @@ namespace: data subset: data def: "A value representing estimated statistical significance of some observed data; typically sequence database hits." [http://edamontology.org] is_a: EDAM_data:1772 ! Score or penalty -is_a: EDAM_data:2914 ! Sequence feature metadata +is_a: EDAM_data:2914 ! Sequence features metadata [Term] id: EDAM_data:0865 @@ -15853,7 +16578,7 @@ namespace: data subset: data def: "Data concerning a biological ontology." [http://edamontology.org] is_a: EDAM_data:2337 ! Metadata -relationship: has_topic EDAM_topic:0089 ! Ontologies +relationship: has_topic EDAM_topic:0089 ! Ontology [Term] id: EDAM_data:2193 @@ -16054,7 +16779,6 @@ consider: EDAM_data:1678 ! Tool log id: EDAM_data:1685 name: EMBOSS supermatcher error file namespace: data - subset: data def: "EMBOSS (EMBASSY) supermatcher error file." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} @@ -16207,7 +16931,7 @@ comment: The forward or 'top' strand might specify a sequence is to be used as g synonym: "DNA strand specification" EXACT [http://edamontology.org] synonym: "Strand" EXACT [http://edamontology.org] is_a: EDAM_data:2534 ! Sequence parameter -is_a: EDAM_data:2914 ! Sequence feature metadata +is_a: EDAM_data:2914 ! Sequence features metadata [Term] @@ -16216,7 +16940,7 @@ name: Translation frame specification namespace: data subset: data def: "Frame for translation of DNA (3 forward and 3 reverse frames relative to a chromosome)." [http://edamontology.org] -is_a: EDAM_data:2534 ! Sequence parameter3 +is_a: EDAM_data:2534 ! Sequence parameter [Term] @@ -16227,7 +16951,7 @@ subset: data def: "Phase for translation of DNA (0, 1 or 2) relative to a fragment of the coding sequence." [http://edamontology.org] synonym: "Phase" EXACT [http://edamontology.org] is_a: EDAM_data:2534 ! Sequence parameter -is_a: EDAM_data:2914 ! Sequence feature metadata +is_a: EDAM_data:2914 ! Sequence features metadata [Term] @@ -16477,7 +17201,7 @@ namespace: data subset: data def: "An offset for a single-point sequence position." [http://edamontology.org] is_a: EDAM_data:1016 ! Sequence position -is_a: EDAM_data:2914 ! Sequence feature metadata +is_a: EDAM_data:2914 ! Sequence features metadata [Term] id: EDAM_data:1017 @@ -17059,7 +17783,7 @@ def: "An image from a microarray experiment which (typically) allows a visualisa synonym: "Gene expression image" EXACT [http://edamontology.org] is_a: EDAM_data:2603 ! Microarray data is_a: EDAM_data:2968 ! Image -relationship: has_topic EDAM_topic:0197 ! Gene expression resources +relationship: has_topic EDAM_topic:0200 ! Microarrays [Term] id: EDAM_data:1714 @@ -17112,7 +17836,7 @@ subset: data ! alt_id: EDAM_data:2221 def: "An ontology of biological or bioinformatics concepts and relations, a controlled vocabulary, structured glossary etc." [http://edamontology.org] is_a: EDAM_data:3031 ! Core data -relationship: has_topic EDAM_topic:0089 ! Ontologies +relationship: has_topic EDAM_topic:0089 ! Ontology [Term] @@ -17123,7 +17847,7 @@ subset: data def: "A concept from a biological ontology." [http://edamontology.org] comment: This includes any fields from the concept definition such as concept name, definition, comments and so on. is_a: EDAM_data:3031 ! Core data -relationship: has_topic EDAM_topic:0089 ! Ontologies +relationship: has_topic EDAM_topic:0089 ! Ontology [Term] @@ -17142,7 +17866,7 @@ namespace: data subset: data def: "Data concerning or derived from a concept from a biological ontology." [http://edamontology.org] is_a: EDAM_data:2337 ! Metadata -relationship: has_topic EDAM_topic:0089 ! Ontologies +relationship: has_topic EDAM_topic:0089 ! Ontology [Term] @@ -17688,7 +18412,6 @@ id: EDAM_data:2779 name: Stock number namespace: identifier subset: identifiers - subset: data def: "An identifier of stock from a catalogue of biological resources." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) @@ -17747,8 +18470,8 @@ subset: identifiers subset: data def: "Name or other identifier of molecular sequence feature(s)." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) -is_a: EDAM_data:2914 ! Sequence feature metadata -relationship: is_identifier_of EDAM_data:1255 ! Sequence features +is_a: EDAM_data:2914 ! Sequence features metadata +relationship: is_identifier_of EDAM_data:1255 ! Feature record [Term] id: EDAM_data:1023 @@ -18300,7 +19023,7 @@ subset: identifiers subset: data def: "Identifier of an entry from a database of microarray data." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) -relationship: is_identifier_of EDAM_data:0931 ! Microarray experiment annotation +relationship: is_identifier_of EDAM_data:0931 ! Experiment annotation (microarray) [Term] id: EDAM_data:1079 @@ -18336,7 +19059,7 @@ subset: data def: "Identifier of an entry from a database of genotypes and phenotypes." [http://edamontology.org] is_a: EDAM_data:0976 ! Identifier (typed) is_a: EDAM_data:2091 ! Accession -relationship: is_identifier_of EDAM_data:0920 ! Genotype and phenotype annotation +relationship: is_identifier_of EDAM_data:0920 ! Genotype/phenotype annotation [Term] @@ -18794,198 +19517,198 @@ consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2672 -name: Ensembl ID ("Bos taurus") +name: Ensembl ID ('Bos taurus') namespace: identifier subset: identifiers subset: data -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Bos taurus" division)." [http://edamontology.org] +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Bos taurus' division)." [http://edamontology.org] regex: "ENSBTA([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2673 -name: Ensembl ID ("Canis familiaris") +name: Ensembl ID ('Canis familiaris') namespace: identifier subset: identifiers subset: data -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Canis familiaris" division)." [http://edamontology.org] +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Canis familiaris' division)." [http://edamontology.org] regex: "ENSCAF([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2674 -name: Ensembl ID ("Cavia porcellus") +name: Ensembl ID ('Cavia porcellus') namespace: identifier subset: identifiers subset: data -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Cavia porcellus" division)." [http://edamontology.org] +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Cavia porcellus' division)." [http://edamontology.org] regex: "ENSCPO([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2675 -name: Ensembl ID ("Ciona intestinalis") +name: Ensembl ID ('Ciona intestinalis') namespace: identifier subset: identifiers subset: data -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Ciona intestinalis" division)." [http://edamontology.org] +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona intestinalis' division)." [http://edamontology.org] regex: "ENSCIN([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2676 -name: Ensembl ID ("Ciona savignyi") +name: Ensembl ID ('Ciona savignyi') namespace: identifier subset: identifiers subset: data -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Ciona savignyi" division)." [http://edamontology.org] +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ciona savignyi' division)." [http://edamontology.org] regex: "ENSCSAV([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2677 -name: Ensembl ID ("Danio rerio") +name: Ensembl ID ('Danio rerio') namespace: identifier subset: identifiers subset: data -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Danio rerio" division)." [http://edamontology.org] +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Danio rerio' division)." [http://edamontology.org] regex: "ENSDAR([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2678 -name: Ensembl ID ("Dasypus novemcinctus") +name: Ensembl ID ('Dasypus novemcinctus') namespace: identifier subset: identifiers subset: data -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Dasypus novemcinctus" division)." [http://edamontology.org] +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Dasypus novemcinctus' division)." [http://edamontology.org] regex: "ENSDNO([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2679 -name: Ensembl ID ("Echinops telfairi") +name: Ensembl ID ('Echinops telfairi') namespace: identifier subset: identifiers subset: data -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Echinops telfairi" division)." [http://edamontology.org] +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Echinops telfairi' division)." [http://edamontology.org] regex: "ENSETE([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2680 -name: Ensembl ID ("Erinaceus europaeus") +name: Ensembl ID ('Erinaceus europaeus') namespace: identifier subset: identifiers subset: data -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Erinaceus europaeus" division)." [http://edamontology.org] +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Erinaceus europaeus' division)." [http://edamontology.org] regex: "ENSEEU([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2681 -name: Ensembl ID ("Felis catus") +name: Ensembl ID ('Felis catus') namespace: identifier subset: identifiers subset: data -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Felis catus" division)." [http://edamontology.org] +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Felis catus' division)." [http://edamontology.org] regex: "ENSFCA([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2682 -name: Ensembl ID ("Gallus gallus") +name: Ensembl ID ('Gallus gallus') namespace: identifier subset: identifiers subset: data -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Gallus gallus" division)." [http://edamontology.org] +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gallus gallus' division)." [http://edamontology.org] regex: "ENSGAL([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2683 -name: Ensembl ID ("Gasterosteus aculeatus") +name: Ensembl ID ('Gasterosteus aculeatus') namespace: identifier subset: identifiers subset: data -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Gasterosteus aculeatus" division)." [http://edamontology.org] +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Gasterosteus aculeatus' division)." [http://edamontology.org] regex: "ENSGAC([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2684 -name: Ensembl ID ("Homo sapiens") +name: Ensembl ID ('Homo sapiens') namespace: identifier subset: identifiers subset: data -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Homo sapiens" division)." [http://edamontology.org] +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Homo sapiens' division)." [http://edamontology.org] regex: "ENSHUM([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2685 -name: Ensembl ID ("Loxodonta africana") +name: Ensembl ID ('Loxodonta africana') namespace: identifier subset: identifiers subset: data -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Loxodonta africana" division)." [http://edamontology.org] +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Loxodonta africana' division)." [http://edamontology.org] regex: "ENSLAF([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2686 -name: Ensembl ID ("Macaca mulatta") +name: Ensembl ID ('Macaca mulatta') namespace: identifier subset: identifiers subset: data -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Macaca mulatta" division)." [http://edamontology.org] +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Macaca mulatta' division)." [http://edamontology.org] regex: "ENSMMU([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2687 -name: Ensembl ID ("Monodelphis domestica") +name: Ensembl ID ('Monodelphis domestica') namespace: identifier subset: identifiers subset: data -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Monodelphis domestica" division)." [http://edamontology.org] +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Monodelphis domestica' division)." [http://edamontology.org] regex: "ENSMOD([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2688 -name: Ensembl ID ("Mus musculus") +name: Ensembl ID ('Mus musculus') namespace: identifier subset: identifiers subset: data -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Mus musculus" division)." [http://edamontology.org] +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Mus musculus' division)." [http://edamontology.org] regex: "ENSMUS([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2689 -name: Ensembl ID ("Myotis lucifugus") +name: Ensembl ID ('Myotis lucifugus') namespace: identifier subset: identifiers subset: data -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Myotis lucifugus" division)." [http://edamontology.org] +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Myotis lucifugus' division)." [http://edamontology.org] regex: "ENSMLU([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID @@ -18996,106 +19719,106 @@ name: Ensembl ID ("Ornithorhynchus anatinus") namespace: identifier subset: identifiers subset: data -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Ornithorhynchus anatinus" division)." [http://edamontology.org] +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Ornithorhynchus anatinus' division)." [http://edamontology.org] regex: "ENSOAN([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2691 -name: Ensembl ID ("Oryctolagus cuniculus") +name: Ensembl ID ('Oryctolagus cuniculus') namespace: identifier subset: identifiers subset: data -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Oryctolagus cuniculus" division)." [http://edamontology.org] +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryctolagus cuniculus' division)." [http://edamontology.org] regex: "ENSOCU([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2692 -name: Ensembl ID ("Oryzias latipes") +name: Ensembl ID ('Oryzias latipes') namespace: identifier subset: identifiers subset: data -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Oryzias latipes" division)." [http://edamontology.org] +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Oryzias latipes' division)." [http://edamontology.org] regex: "ENSORL([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2693 -name: Ensembl ID ("Otolemur garnettii") +name: Ensembl ID ('Otolemur garnettii') namespace: identifier subset: identifiers subset: data -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Otolemur garnettii" division)." [http://edamontology.org] +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Otolemur garnettii' division)." [http://edamontology.org] regex: "ENSSAR([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2694 -name: Ensembl ID ("Pan troglodytes") +name: Ensembl ID ('Pan troglodytes') namespace: identifier subset: identifiers subset: data -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Pan troglodytes" division)." [http://edamontology.org] +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Pan troglodytes' division)." [http://edamontology.org] regex: "ENSPTR([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2695 -name: Ensembl ID ("Rattus norvegicus") +name: Ensembl ID ('Rattus norvegicus') namespace: identifier subset: identifiers subset: data -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Rattus norvegicus" division)." [http://edamontology.org] +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Rattus norvegicus' division)." [http://edamontology.org] regex: "ENSRNO([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2696 -name: Ensembl ID ("Spermophilus tridecemlineatus") +name: Ensembl ID ('Spermophilus tridecemlineatus') namespace: identifier subset: identifiers subset: data -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Spermophilus tridecemlineatus" division)." [http://edamontology.org] +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Spermophilus tridecemlineatus' division)." [http://edamontology.org] regex: "ENSSTO([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2697 -name: Ensembl ID ("Takifugu rubripes") +name: Ensembl ID ('Takifugu rubripes') namespace: identifier subset: identifiers subset: data -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Takifugu rubripes" division)." [http://edamontology.org] +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Takifugu rubripes' division)." [http://edamontology.org] regex: "ENSFRU([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2698 -name: Ensembl ID ("Tupaia belangeri") +name: Ensembl ID ('Tupaia belangeri') namespace: identifier subset: identifiers subset: data -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Tupaia belangeri" division)." [http://edamontology.org] +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Tupaia belangeri' division)." [http://edamontology.org] regex: "ENSTBE([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID [Term] id: EDAM_data:2699 -name: Ensembl ID ("Xenopus tropicalis") +name: Ensembl ID ('Xenopus tropicalis') namespace: identifier subset: identifiers subset: data -def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ("Xenopus tropicalis" division)." [http://edamontology.org] +def: "Identifier of an entry (exon, gene, transcript or protein) from the Ensembl 'core' database ('Xenopus tropicalis' division)." [http://edamontology.org] regex: "ENSXET([EGTP])[0-9]{11}" is_obsolete: true !{since=beta12orEarlier} consider: EDAM_data:2610 ! Ensembl ID @@ -19973,7 +20696,7 @@ subset: data def: "Name of a chromosome." [http://edamontology.org] is_a: EDAM_data:2119 ! Nucleic acid identifier is_a: EDAM_data:0984 ! Molecule name -relationship: is_identifier_of EDAM_data:0919 ! Nucleic acid features (chromosome) +relationship: is_identifier_of EDAM_data:0919 ! Gene annotation (chromosome) [Term] id: EDAM_data:2208 @@ -20308,7 +21031,7 @@ synonym: "Enzyme Commission number" EXACT [http://edamontology.org] xref: Moby:EC_Number xref: Moby:Annotated_EC_Number regex: "[0-9]+\.-\.-\.-|[0-9]+\.[0-9]+\.-\.-|[0-9]+\.[0-9]+\.[0-9]+\.-|[0-9]+\.[0-9]+\.[0-9]+\.[0-9]+" -is_a: EDAM_data:2321 ! Enzyme accession +is_a: EDAM_data:2321 ! Enzyme ID [Term] id: EDAM_data:2107 @@ -20349,7 +21072,7 @@ namespace: identifier subset: identifiers subset: data def: "Identifier of an enzyme from the REBASE enzymes database." [http://edamontology.org] -is_a: EDAM_data:2091 ! Enzyme accession +is_a: EDAM_data:2321 ! Enzyme ID [Term] @@ -20679,7 +21402,7 @@ subset: data def: "Any name (other than the recommended one) for a gene." [http://edamontology.org] synonym: "Gene name synonym" EXACT [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1026 ! Gene name +consider: EDAM_data:1026 ! Gene symbol [Term] @@ -20969,7 +21692,7 @@ subset: identifiers subset: data def: "An NCBI RefSeq unique identifier of a gene." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1027 ! NCBI gene ID +consider: EDAM_data:1027 ! Gene ID (NCBI) [Term] id: EDAM_data:1029 @@ -20990,7 +21713,7 @@ subset: data def: "An Entrez unique identifier of a gene." [http://edamontology.org] regex: "[0-9]+" is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_data:1027 ! NCBI gene ID +consider: EDAM_data:1027 ! Gene ID (NCBI) [Term] @@ -21901,7 +22624,7 @@ def: "A persistent, unique identifier of a molecular sequence database entry." [ synonym: "Sequence accession number" EXACT [http://edamontology.org] is_a: EDAM_data:1063 ! Sequence identifier is_a: EDAM_data:2091 ! Accession -is_a: EDAM_data:2914 ! Sequence feature metadata +is_a: EDAM_data:2914 ! Sequence features metadata [Term] @@ -21948,7 +22671,7 @@ subset: data def: "An identifier of PIR sequence database entry." [http://edamontology.org] synonym: "PIR accession number" EXACT [http://edamontology.org] synonym: "PIR ID" EXACT [http://edamontology.org] -is_a: EDAM_data:1096 ! Sequence identifier (protein) +is_a: EDAM_data:1096 ! Sequence accession (protein) relationship: is_identifier_of EDAM_data:0849 ! Sequence record [Term] @@ -21971,7 +22694,7 @@ subset: identifiers subset: data def: "Identifier of a protein sequence from the TAIR database." [http://edamontology.org] regex: "AASequence:[0-9]{10}" -is_a: EDAM_data:1096 ! Sequence identifier (protein) +is_a: EDAM_data:1096 ! Sequence accession (protein) is_a: EDAM_data:2387 ! TAIR accession relationship: is_identifier_of EDAM_data:0849 ! Sequence record @@ -22068,7 +22791,7 @@ subset: data def: "Accession number of a nucleotide sequence database entry." [http://edamontology.org] synonym: "Nucleotide sequence accession number" EXACT [http://edamontology.org] is_a: EDAM_data:1093 ! Sequence accession -relationship: is_identifier_of EDAM_data:2977 ! Nucleotide sequence +relationship: is_identifier_of EDAM_data:2977 ! Nucleic acid sequence [Term] @@ -22146,7 +22869,7 @@ namespace: identifier subset: identifiers subset: data def: "Accession number of a UniProt (protein sequence) database entry. May contain version or isoform number." [http://edamontology.org] -regex: "[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]" "[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]" "[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9].[0-9]+" "[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9].[0-9]+" "[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]-[0-9]+" "[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]-[0-9]+" +regex: "[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]" "[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]" "[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9].[0-9]+" "[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9].[0-9]+" "[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]-[0-9]+" "[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]-[0-9]+" example: "Q7M1G0" "P43353-2" "P01012.107" ! is_a: EDAM_data:3021 ! UniProt accession ! relationship: is_identifier_of EDAM_format:1208 ! Protein sequence ! now 'protein' format @@ -23929,7 +24652,6 @@ synonym: "TXT" NARROW [http://filext.com/file-extension/TXT] synonym: "Text File" NARROW [http://filext.com/file-extension/TXT] synonym: "TSV" NARROW [http://filext.com/file-extension/TSV] synonym: "Tab-Separated Values" NARROW [http://filext.com/file-extension/TSV] -synonym: "Symbol sequence" RELATED [http://www.onto-med.de/ontologies/gfo.owl#Symbol_sequence] is_a: EDAM_format:1915 ! Format [Term] @@ -24055,7 +24777,7 @@ namespace: format subset: formats def: "Data format for molecular sequence feature information." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:1255 ! Sequence features +relationship: is_format_of EDAM_data:1255 ! Feature record [Term] id: EDAM_format:1921 @@ -24294,7 +25016,7 @@ namespace: format subset: formats def: "Format for protein interaction data." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:0906 ! Protein report (interaction) +relationship: is_format_of EDAM_data:0906 ! Protein interaction [Term] @@ -24332,7 +25054,7 @@ subset: formats def: "Format of a report on genotype / phenotype information." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} consider: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:0920 ! Genotype and phenotype annotation +relationship: is_format_of EDAM_data:0920 ! Genotype/phenotype annotation [Term] id: EDAM_format:2060 @@ -24459,7 +25181,7 @@ namespace: format subset: formats def: "Format for secondary structure (predicted or real) of an RNA molecule." [http://edamontology.org] is_a: EDAM_format:2350 ! Format (typed) -relationship: is_format_of EDAM_data:0880 ! RNA secondary structure +relationship: is_format_of EDAM_data:0880 ! RNA secondary structure record [Term] id: EDAM_format:2078 @@ -24651,7 +25373,7 @@ namespace: format subset: formats def: "Clustalw output format." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:1982 ! clustal alignment format +consider: EDAM_format:1982 ! clustal [Term] id: EDAM_format:1925 @@ -24706,7 +25428,7 @@ namespace: format subset: formats def: "GFF3 feature file format with sequence." [http://edamontology.org] is_a: EDAM_format:2551 ! Sequence record format (text) -is_a: EDAM_format:1975 ! GFF2 +is_a: EDAM_format:1975 ! GFF3 [Term] @@ -24872,7 +25594,7 @@ namespace: format subset: formats def: "Selex sequence format." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:2000 ! selex alignment format +consider: EDAM_format:2000 ! selex [Term] @@ -25009,7 +25731,6 @@ namespace: format subset: formats def: "A text format resembling FASTA format." [http://edamontology.org] comment: This concept may also be used for the many non-standard FASTA-like formats. -synonym: "FASTA" EXACT [http://filext.com/file-extension/FASTA] !{note="fileext.com synonyms are in general narrower in the sense of being defined only as file formats, as opposed to data formats."} synonym: "DNA and Protein Sequence Alignment" NARROW [http://filext.com/file-extension/FASTA] is_a: EDAM_format:2546 ! FASTA-like is_a: EDAM_format:2330 ! Textual format @@ -25111,7 +25832,7 @@ namespace: format subset: formats def: "A text format resembling EMBL entry format." [http://edamontology.org] comment: This concept may be used for the many non-standard EMBL-like text formats. -is_a: EDAM_format:2543 ! EMBL-like +is_a: EDAM_format:2543 ! EMBL-like format is_a: EDAM_format:2330 ! Textual format [Term] @@ -25121,7 +25842,7 @@ namespace: format subset: formats def: "An XML format resembling EMBL entry format." [http://edamontology.org] comment: This concept may be used for the any non-standard EMBL-like XML formats. -is_a: EDAM_format:2543 ! EMBL-like +is_a: EDAM_format:2543 ! EMBL-like format is_a: EDAM_format:2332 ! XML [Term] @@ -25130,7 +25851,7 @@ name: EMBL-HTML namespace: format subset: formats def: "EMBL entry format wrapped in HTML elements." [http://edamontology.org] -is_a: EDAM_format:2543 ! EMBL-like +is_a: EDAM_format:2543 ! EMBL-like format is_a: EDAM_format:2331 ! HTML @@ -25168,7 +25889,7 @@ name: EMBLXML namespace: format subset: formats def: "XML format for EMBL entries." [http://edamontology.org] -is_a: EDAM_format:2204 ! EMBL (XML) +is_a: EDAM_format:2204 ! EMBL format (XML) [Term] @@ -25177,7 +25898,7 @@ name: cdsxml namespace: format subset: formats def: "XML format for EMBL entries." [http://edamontology.org] -is_a: EDAM_format:2204 ! EMBL (XML) +is_a: EDAM_format:2204 ! EMBL format (XML) [Term] id: EDAM_format:2185 @@ -25185,7 +25906,7 @@ name: insdxml namespace: format subset: formats def: "XML format for EMBL entries." [http://edamontology.org] -is_a: EDAM_format:2204 ! EMBL (XML) +is_a: EDAM_format:2204 ! EMBL format (XML) [Term] @@ -25233,7 +25954,7 @@ name: uniprotkb-like (text) namespace: format subset: formats def: "A text sequence format resembling uniprotkb entry format." [http://edamontology.org] -is_a: EDAM_format:2547 ! uniprotkb-like +is_a: EDAM_format:2547 ! uniprotkb-like format is_a: EDAM_format:2330 ! Textual format @@ -25321,7 +26042,7 @@ namespace: format subset: formats def: "A text format resembling FASTQ short read format." [http://edamontology.org] comment: This concept may be used for non-standard FASTQ short read-like formats. -is_a: EDAM_format:2545 ! FASTQ-like +is_a: EDAM_format:2545 ! FASTQ-like format is_a: EDAM_format:2330 ! Textual format [Term] @@ -25330,7 +26051,7 @@ name: FASTQ namespace: format subset: formats def: "FASTQ short read format ignoring quality scores." [http://edamontology.org] -is_a: EDAM_format:2182 ! FASTQ-like (text) +is_a: EDAM_format:2182 ! FASTQ-like format (text) [Term] id: EDAM_format:1931 @@ -25338,7 +26059,7 @@ name: FASTQ-illumina namespace: format subset: formats def: "FASTQ Illumina 1.3 short read format." [http://edamontology.org] -is_a: EDAM_format:2182 ! FASTQ-like (text) +is_a: EDAM_format:2182 ! FASTQ-like format (text) [Term] id: EDAM_format:1932 @@ -25346,7 +26067,7 @@ name: FASTQ-sanger namespace: format subset: formats def: "FASTQ short read format with phred quality." [http://edamontology.org] -is_a: EDAM_format:2182 ! FASTQ-like (text) +is_a: EDAM_format:2182 ! FASTQ-like format (text) [Term] id: EDAM_format:1933 @@ -25354,7 +26075,7 @@ name: FASTQ-solexa namespace: format subset: formats def: "FASTQ Solexa/Illumina 1.0 short read format." [http://edamontology.org] -is_a: EDAM_format:2182 ! FASTQ-like (text) +is_a: EDAM_format:2182 ! FASTQ-like format (text) [Term] id: EDAM_format:2548 @@ -25363,7 +26084,7 @@ namespace: format subset: formats def: "Format for a sequence feature table." [http://edamontology.org] is_a: EDAM_format:1920 ! Sequence feature annotation format -relationship: is_format_of EDAM_data:1255 ! Sequence features +relationship: is_format_of EDAM_data:1255 ! Feature record [Term] id: EDAM_format:1979 @@ -25417,7 +26138,7 @@ namespace: format subset: formats def: "Swiss-Prot feature format." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:1963 ! swiss +consider: EDAM_format:1963 ! Swiss-Prot format [Term] @@ -25427,7 +26148,7 @@ namespace: format subset: formats def: "EMBL feature format." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:1927 ! EMBL +consider: EDAM_format:1927 ! EMBL format [Term] @@ -25437,7 +26158,7 @@ namespace: format subset: formats def: "Genbank feature format." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:1936 ! GenBank +consider: EDAM_format:1936 ! GenBank format [Term] @@ -25633,7 +26354,7 @@ namespace: format subset: formats def: "Nexus/paup format for (aligned) sequences." [http://edamontology.org] is_obsolete: true !{since=beta12orEarlier} -consider: EDAM_format:1949 ! nexus +consider: EDAM_format:1949 ! nexus-seq [Term] id: EDAM_format:1995 @@ -26659,7 +27380,7 @@ namespace: format subset: formats def: "Format of phylogenetic cliques data." [http://edamontology.org] is_a: EDAM_format:2036 ! Phylogenetic character data format -relationship: is_format_of EDAM_data:1428 ! Phylogenetic tree report (cliques) +relationship: is_format_of EDAM_data:1428 ! Phylogenetic character cliques [Term] @@ -26669,7 +27390,7 @@ namespace: format subset: formats def: "Format of phylogenetic invariants data." [http://edamontology.org] is_a: EDAM_format:2036 ! Phylogenetic character data format -relationship: is_format_of EDAM_data:1429 ! Phylogenetic tree report (invariants) +relationship: is_format_of EDAM_data:1429 ! Phylogenetic invariants [Term] id: EDAM_format:1430 @@ -27427,8 +28148,7 @@ name: Vienna local RNA secondary structure namespace: format subset: formats def: "Format of local RNA secondary structure components with free energy values, generated by the Vienna program." [http://edamontology.org] -synonym: "Dot-bracket format" EXACT [http://edamontology.org] -is_a: EDAM_format:2076 ! RNA secondary structure format +is_a: EDAM_format:1457 ! Vienna RNA secondary structure is_a: EDAM_format:2330 ! Textual format [Term] @@ -27822,7 +28542,7 @@ namespace: format subset: formats def: "Alphabet for a molecular sequence with possible unknown positions but without ambiguity or non-sequence characters." [http://edamontology.org] is_a: EDAM_format:2094 ! pure -is_a: EDAM_format:2096 ! unambiguous +is_a: EDAM_format:2096 ! unambiguous sequence [Term] id: EDAM_format:2567