diff --git a/EDAM_dev.owl b/EDAM_dev.owl index 0b74c1d..cd9497c 100644 --- a/EDAM_dev.owl +++ b/EDAM_dev.owl @@ -41,11 +41,11 @@ operations "EDAM operations" Bioinformatics operations, data types, formats, identifiers and topics EDAM http://edamontology.org/ "EDAM relations and concept properties" + 3770 application/rdf+xml 12.05.2016 18:23 GMT EDAM_data http://edamontology.org/data_ "EDAM types of data" concept_properties "EDAM concept properties" - 3766 EDAM is an ontology of well established, familiar concepts that are prevalent within bioinformatics, including types of data and data identifiers, data formats, operations and topics. EDAM is a simple ontology - essentially a set of terms with synonyms and definitions - organised into an intuitive hierarchy for convenient use by curators, software developers and end-users. EDAM is suitable for large-scale semantic annotations and categorisation of diverse bioinformatics resources. EDAM is also suitable for diverse application including for example within workbenches and workflow-management systems, software distributions, and resource registries. Jon Ison Matúš Kalaš @@ -418,16 +418,16 @@ - Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:bearer_of' is narrower in the sense that it only relates ontological categories (concepts) that are an 'independent_continuant' (snap:IndependentContinuant) with ontological categories that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant), and broader in the sense that it relates with any borne objects not just functions of the subject. - OBO_REL:bearer_of + In very unusual cases. + true - + - true - In very unusual cases. + OBO_REL:bearer_of + Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:bearer_of' is narrower in the sense that it only relates ontological categories (concepts) that are an 'independent_continuant' (snap:IndependentContinuant) with ontological categories that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant), and broader in the sense that it relates with any borne objects not just functions of the subject. - + @@ -471,17 +471,17 @@ - true - In very unusual cases. - - - - OBO_REL:has_participant 'OBO_REL:has_participant' is narrower in the sense that it only relates ontological categories (concepts) that are a 'process' (span:Process) with ontological categories that are a 'continuant' (snap:Continuant), and broader in the sense that it relates with any participating objects not just inputs or input arguments of the subject. + + In very unusual cases. + true + + + @@ -547,8 +547,8 @@ - In very unusual cases. true + In very unusual cases. @@ -575,8 +575,8 @@ - OBO_REL:quality_of Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:quality_of' might be seen narrower in the sense that it only relates subjects that are a 'quality' (snap:Quality) with objects that are an 'independent_continuant' (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object. + OBO_REL:quality_of @@ -610,14 +610,14 @@ - true In very unusual cases. + true - OBO_REL:inheres_in Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:inheres_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'specifically_dependent_continuant' (snap:SpecificallyDependentContinuant) with ontological categories that are an 'independent_continuant' (snap:IndependentContinuant), and broader in the sense that it relates any borne subjects not just functions. + OBO_REL:inheres_in @@ -665,17 +665,17 @@ - In very unusual cases. - true - - - - 'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just inputs or input arguments. OBO_REL:participates_in + + In very unusual cases. + true + + + @@ -700,8 +700,8 @@ - 'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just outputs or output arguments. It is also not clear whether an output (result) actually participates in the process that generates it. OBO_REL:participates_in + 'OBO_REL:participates_in' is narrower in the sense that it only relates ontological categories (concepts) that are a 'continuant' (snap:Continuant) with ontological categories that are a 'process' (span:Process), and broader in the sense that it relates any participating subjects not just outputs or output arguments. It is also not clear whether an output (result) actually participates in the process that generates it. @@ -741,17 +741,17 @@ - Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:quality_of' might be seen narrower in the sense that it only relates subjects that are a 'quality' (snap:Quality) with objects that are an 'independent_continuant' (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object. - OBO_REL:quality_of - - - - true In very unusual cases. + + Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:quality_of' might be seen narrower in the sense that it only relates subjects that are a 'quality' (snap:Quality) with objects that are an 'independent_continuant' (snap:IndependentContinuant), and is broader in the sense that it relates any qualities of the object. + OBO_REL:quality_of + + + @@ -806,12 +806,6 @@ - EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). - Data set - - - - Data record EDAM does not distinguish a data record (a tool-understandable information artefact) from data or datum (its content, the tool-understandable encoding of an information). @@ -819,7 +813,13 @@ EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). + Data set + + + + Datum + EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). @@ -5991,8 +5991,8 @@ - UniProt|Enzyme Nomenclature A protein entity has the MIRIAM data type 'UniProt', and an enzyme has the MIRIAM data type 'Enzyme Nomenclature'. + UniProt|Enzyme Nomenclature @@ -9098,13 +9098,13 @@ - + - + beta12orEarlier @@ -10715,8 +10715,8 @@ Heat map - + A graphical 2D tabular representation of gene expression data, typically derived from a DNA microarray experiment. beta12orEarlier A heat map is a table where rows and columns correspond to different genes and contexts (for example, cells or samples) and the cell color represents the level of expression of a gene that context. @@ -14119,13 +14119,13 @@ - + - + Identifier of a codon usage table, for example a genetic code. @@ -17464,7 +17464,7 @@ - Gene expression data + Expression data @@ -17472,10 +17472,13 @@ + Metabolite expression data + Image, hybridisation or some other data arising from a study of expression of an biological entity, for example a gene or protein. + Protein expression data + This is a broad data type and is used a placeholder for other, more specific types. See also http://edamontology.org/data_0931 + Gene expression data beta12orEarlier - Image or hybridisation data for a microarray, typically a study of gene expression. Microarray data - This is a broad data type and is used a placeholder for other, more specific types. See also http://edamontology.org/data_0931 @@ -18331,13 +18334,13 @@ - + - + beta12orEarlier @@ -20392,13 +20395,13 @@ - + - + Identifier of a lipid. @@ -24019,6 +24022,34 @@ + + + + Clustered expression profiles + + Groupings of expression profiles according to a clustering algorithm. + 1.16 + Clustered gene expression profiles + + + + + + + + + + BRENDA ontology ID + + An identifier of a concept from the BRENDA ontology. + 1.16 + + + + + + + @@ -26649,17 +26680,17 @@ - File format - File format denotes only formats of a computer file, but the same formats apply also to data blobs or exchanged messages. - - - - A defined data format has its implicit or explicit data model, and EDAM does not distinguish the two. Some data models however do not have any standard way of serialisation into an exchange format, and those are thus not considered formats in EDAM. (Remark: even broader - or closely related - term to 'Data model' would be an 'Information model'.) Data model + + File format denotes only formats of a computer file, but the same formats apply also to data blobs or exchanged messages. + File format + + + @@ -28678,13 +28709,13 @@ - + - + Data format for the emission and transition counts of a hidden Markov model. @@ -29498,7 +29529,7 @@ - + @@ -29510,7 +29541,7 @@ - + BioXSD XML format @@ -29621,7 +29652,7 @@ uniprotkb-like format - + beta12orEarlier A sequence format resembling uniprotkb entry format. @@ -30003,13 +30034,13 @@ - + - + Format of a bibliographic reference. @@ -33319,6 +33350,21 @@ experiments employing a combination of technologies. + + + + UniProt XML format + + + 1.16 + XML sequence format used for UniProt entries. + + + + + + + @@ -33362,8 +33408,14 @@ experiments employing a combination of technologies. - Computational tool + Function + Operation is a function that is computational. It typically has input(s) and output(s), which are always data. + + + + Computational tool provides one or more operations. + Computational tool @@ -33373,12 +33425,6 @@ experiments employing a combination of technologies. - - Operation is a function that is computational. It typically has input(s) and output(s), which are always data. - Function - - - @@ -33431,14 +33477,14 @@ experiments employing a combination of technologies. - - + + - - + + Annotate an entity (typically a biological or biomedical database entity) with terms from a controlled vocabulary. @@ -33593,14 +33639,14 @@ experiments employing a combination of technologies. - - + + - - + + Calculate sequence ambiguity, for example identity regions in protein or nucleotide sequences with many ambiguity codes. @@ -33619,14 +33665,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -33728,14 +33774,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -33785,14 +33831,14 @@ experiments employing a combination of technologies. - - + + - - + + This might be a residue-level search for properties such as solvent accessibility, hydropathy, secondary structure, ligand-binding etc. @@ -34051,14 +34097,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -34303,14 +34349,14 @@ experiments employing a combination of technologies. - - + + - - + + Predict tertiary structure of a molecular (biopolymer) sequence. @@ -34349,14 +34395,14 @@ experiments employing a combination of technologies. - - + + - - + + Analyse experimental protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc. @@ -34548,14 +34594,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -34609,20 +34655,20 @@ experiments employing a combination of technologies. - - + + - - + + - - + + @@ -34633,8 +34679,8 @@ experiments employing a combination of technologies. - - + + beta12orEarlier @@ -34655,14 +34701,14 @@ experiments employing a combination of technologies. - - + + - - + + Identify and plot third base position variability in a nucleotide sequence. @@ -34694,14 +34740,14 @@ experiments employing a combination of technologies. - - + + - - + + Sequence distance matrix construction @@ -34848,14 +34894,14 @@ experiments employing a combination of technologies. - - + + - - + + Sequence profile construction @@ -34876,13 +34922,13 @@ experiments employing a combination of technologies. - + - + @@ -34908,12 +34954,6 @@ experiments employing a combination of technologies. - - - - - - @@ -34924,6 +34964,12 @@ experiments employing a combination of technologies. + + + + + + Sequence profile alignment Profile-to-profile alignment Methods might perform one-to-one, one-to-many or many-to-many comparisons. See also 'Sequence alignment comparison'. @@ -34942,14 +34988,14 @@ experiments employing a combination of technologies. - - + + - - + + Structural profile alignment @@ -34976,14 +35022,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -35004,14 +35050,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -35125,14 +35171,14 @@ experiments employing a combination of technologies. - - + + - - + + @@ -35182,14 +35228,14 @@ experiments employing a combination of technologies. - - + + - - + + This includes predicting primers based on gene structure, promoters, exon-exon junctions, predicting primers that are conserved across multiple genomes or species, primers for for gene transcription profiling, for genotyping polymorphisms, for example single nucleotide polymorphisms (SNPs), for large scale sequencing, or for methylation PCRs. @@ -35217,8 +35263,8 @@ experiments employing a combination of technologies. - - + + @@ -35229,8 +35275,8 @@ experiments employing a combination of technologies. - - + + @@ -35308,7 +35354,7 @@ experiments employing a combination of technologies. - Gene expression profile clustering + Expression profile clustering @@ -35317,8 +35363,11 @@ experiments employing a combination of technologies. + Gene expression profile clustering + Protein expression profile clustering beta12orEarlier - Perform cluster analysis of gene expression (microarray) data, for example clustering of similar gene expression profiles. + Metabolite expression profile clustering + Perform cluster analysis of expression data to identify groups with similar expression profiles, for example, clustering of similar gene expression profiles. @@ -35355,7 +35404,7 @@ experiments employing a combination of technologies. - Gene expression profile comparison + Expression profile comparison @@ -35364,8 +35413,11 @@ experiments employing a combination of technologies. + Protein expression profile comparison beta12orEarlier - Compare gene expression profiles or patterns. + Gene expression profile comparison + Compare expression profiles or patterns, e.g. a gene expression or some otther type of profiles. + Metabolite expression profile comparison @@ -35528,14 +35580,14 @@ experiments employing a combination of technologies. - - + + - - + + Phylogenetic trees are usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. @@ -35590,13 +35642,13 @@ experiments employing a combination of technologies. - + - + @@ -35747,14 +35799,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -35804,20 +35856,20 @@ experiments employing a combination of technologies. - - + + - + - - + + beta12orEarlier @@ -38082,13 +38134,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - + - + Model the structure of a protein in complex with a small molecule or another macromolecule. @@ -38534,14 +38586,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + RNA secondary structure alignment generation @@ -39935,7 +39987,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern beta12orEarlier Analyse a known network of gene regulation. - @@ -40884,14 +40935,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Structure analysis (protein) @@ -41045,14 +41096,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + This is a broad concept and is used a placeholder for other, more specific concepts. @@ -41389,14 +41440,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Predict a network of gene regulation. @@ -41984,7 +42035,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - + @@ -41996,7 +42047,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - + Simulate molecular (typically protein) conformation using a computational model of physical forces and computer simulation. @@ -42015,14 +42066,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Analyse a nucleic acid sequence (using methods that are only applicable to nucleic acid sequences). @@ -42082,14 +42133,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Analyse nucleic acid tertiary structural data. @@ -42275,14 +42326,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Predict the interactions of proteins with other molecules. @@ -42311,7 +42362,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Gene expression data analysis + Expression data analysis @@ -42319,12 +42370,12 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Gene expression (microarray) data processing - Gene expression profile analysis + Gene expression data analysis + Metabolite expression analysis + Protein expression analysis + Gene expression analysis beta12orEarlier - Microarray data processing - Gene expression data processing - Gene expression analysis + Microarray data analysis Process (read and / or write) gene expression (typically microarray) data, including analysis of one or more gene expression profiles, typically to interpret them in functional terms. @@ -42729,7 +42780,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - + @@ -42741,7 +42792,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - + beta12orEarlier @@ -43079,14 +43130,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + beta12orEarlier @@ -43133,8 +43184,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + @@ -43145,8 +43196,8 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + Analyse a body of scientific text (typically a full text article from a scientific journal.) @@ -43551,14 +43602,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Features includes functional sites or regions, secondary structure, structural domains and so on. Methods might use fingerprints, motifs, profiles, hidden Markov models, sequence alignment etc to provide a mapping of a query protein sequence to a discriminatory element. This includes methods that search a secondary protein database (Prosite, Blocks, ProDom, Prints, Pfam etc.) to assign a protein sequence(s) to a known protein family or group. @@ -43654,14 +43705,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Assembly quality evaluation @@ -44722,13 +44773,13 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - + - + 1.4 @@ -46431,6 +46482,49 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp + + + + Weighted correlation network analysis + + + + + + + + A data mining method typically used for studying biological networks based on pairwise correlations between variables. + 1.16 + WGCNA + Weighted gene co-expression network analysis + + + + + + + + + + Protein identification + + + + + + + + + Peptide-spectrum-matching + Protein inference + Identification of protein, for example from one or more peptide identifications by tandem mass spectrometry. + 1.16 + + + + + + @@ -51789,6 +51883,7 @@ positional features such as functional sites in nucleotide sequences. Drug formulation and delivery + Biotherapeutics The process of formulating abd administering a pharmaceutical compound to achieve a therapeutic effect. Drug delivery Drug formulation @@ -52612,6 +52707,7 @@ positional features such as functional sites in nucleotide sequences.VT 1.3.2 Data mining The discovery of patterns in large data sets and the extraction and trasnsformation of those patterns into a useful format. true + Pattern recognition KDD Knowledge discovery in databases