From fd3c2853c3d741709bb86210c3d191ca69608dc3 Mon Sep 17 00:00:00 2001 From: matuskalas Date: Tue, 1 Nov 2016 03:50:16 +0100 Subject: [PATCH] History of releases: 1.15 --- releases/EDAM.owl | 1046 ++++++++++++++++++++++++++++++++++------------------- 1 file changed, 675 insertions(+), 371 deletions(-) diff --git a/releases/EDAM.owl b/releases/EDAM.owl index b0b3ee1..7869a27 100644 --- a/releases/EDAM.owl +++ b/releases/EDAM.owl @@ -28,6 +28,9 @@ xmlns:doap="http://usefulinc.com/ns/doap#" xmlns:edam="&oboOther;edam#"> + 1.15 + 12.05.2016 18:23 GMT + 3751 EDAM_topic http://edamontology.org/topic_ "EDAM topics" EDAM_operation http://edamontology.org/operation_ "EDAM operations" formats "EDAM data formats" @@ -45,12 +48,9 @@ EDAM_data http://edamontology.org/data_ "EDAM types of data" concept_properties "EDAM concept properties" Jon Ison - 3730 Matúš Kalaš EDAM_format http://edamontology.org/format_ "EDAM data formats" - 1.14 topics "EDAM topics" - 24:02:2016 21:54GMT Hervé Ménager 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 categorization 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. @@ -418,8 +418,8 @@ - In very unusual cases. true + In very unusual cases. @@ -465,16 +465,16 @@ - 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. - + - '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. - OBO_REL:has_participant + true + In very unusual cases. - + @@ -505,8 +505,8 @@ - true In very unusual cases. + true @@ -541,8 +541,8 @@ - true In very unusual cases. + true @@ -598,22 +598,22 @@ - 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:function_of Is defined anywhere? Not in the 'unknown' version of RO. 'OBO_REL:function_of' only relates subjects that are a 'function' (snap:Function) with objects that are an 'independent_continuant' (snap:IndependentContinuant), so for example no processes. It does not define explicitly that the subject is a function of the object. + OBO_REL:function_of - 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. + true + In very unusual cases. - + @@ -694,14 +694,14 @@ - '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. - In very unusual cases. true + In very unusual cases. @@ -741,8 +741,8 @@ - In very unusual cases. true + In very unusual cases. @@ -800,22 +800,22 @@ - 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). - Data record + EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). + Data set - + - EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). Datum + EDAM does not distinguish the multiplicity of data, such as one data item (datum) versus a collection of data (data set). - 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). - + @@ -1278,7 +1278,7 @@ - + http://en.wikipedia.org/wiki/Sequence_alignment @@ -1637,7 +1637,7 @@ - + Alignment (superimposition) of molecular tertiary (3D) structures. @@ -2644,7 +2644,7 @@ - + An index of data of biological relevance. @@ -2663,7 +2663,7 @@ - + A report of an analysis of an index of biological data. @@ -2825,8 +2825,7 @@ Moby:BooleanQueryString Moby:Wildcard_Query Moby:Global_Keyword - Terms - Text + Term @@ -3645,9 +3644,11 @@ Sequence feature label + + + A name of a sequence feature, e.g. the name of a feature to be displayed to an end-user. Typically an EMBL or Swiss-Prot feature label. Sequence feature name - Typically an EMBL or Swiss-Prot feature label. 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. beta12orEarlier @@ -5998,8 +5999,8 @@ - A protein entity has the MIRIAM data type 'UniProt', and an enzyme has the MIRIAM data type 'Enzyme Nomenclature'. UniProt|Enzyme Nomenclature + A protein entity has the MIRIAM data type 'UniProt', and an enzyme has the MIRIAM data type 'Enzyme Nomenclature'. @@ -8023,10 +8024,11 @@ Hidden Markov model + HMM beta12orEarlier - A hidden Markov model representation of a set or alignment of sequences. + A statistical Markov model of a system which is assumed to be a Markov process with unobserved (hidden) states. For example, a hidden Markov model representation of a set or alignment of sequences. @@ -9112,13 +9114,13 @@ - + - + beta12orEarlier @@ -11377,7 +11379,7 @@ - + An informative report on a specific drug. @@ -14083,7 +14085,7 @@ - + beta12orEarlier @@ -14175,13 +14177,13 @@ - + - + Identifier of a codon usage table, for example a genetic code. @@ -18402,13 +18404,13 @@ - + - + beta12orEarlier @@ -19053,9 +19055,9 @@ - GO concept ID (cellular compartment) + GO concept ID (cellular component) - An identifier of a 'cellular compartment' concept from the Gene Ontology. + An identifier of a 'cellular component' concept from the Gene Ontology. [0-9]{7}|GO:[0-9]{7} beta12orEarlier GO concept identifier (cellular compartment) @@ -20464,13 +20466,13 @@ - + - + Identifier of a lipid. @@ -22362,13 +22364,13 @@ Sequence feature name - - + + 1.15 A name of a sequence feature, e.g. the name of a feature to be displayed to an end-user. + true beta13 - - - + + @@ -23270,10 +23272,13 @@ Hidden Markov model - + A statistical Markov model of a system which is assumed to be a Markov process with unobserved (hidden) states. 1.4 - + true + 1.15 + + @@ -23296,10 +23301,8 @@ Raw image 1.5 - Amino acid data http://semanticscience.org/resource/SIO_000081 beta12orEarlier - Image data Raw biological or biomedical image generated by some experimental technique. @@ -23520,8 +23523,6 @@ RNA sequence - A DNA sequence. - DNA sequences RNA sequences 1.8 @@ -23618,7 +23619,6 @@ This can include basic provenance and technical information about the image, scientific annotation and so on. Any data concerning a specific biological or biomedical image. 1.9 - Image data Image-related data @@ -23756,7 +23756,9 @@ Biodiversity report + Biodiversity information + OTU table 1.9 A report about biodiversity data. @@ -23894,6 +23896,131 @@ + + + + Sequencing metadata name + + 1.15 + Data concerning a sequencing experiment, that may be specified as an input to some tool. + + + + + + + + + + Flow cell identifier + + A flow cell is used to immobilise, amplify and sequence millions of molecules at once. In Illumina machines, a flowcell is composed of 8 "lanes" which allows 8 experiments in a single analysis. + An identifier of a flow cell of a sequencing machine. + 1.15 + + + + + + + + + + Lane identifier + + An identifier of a lane within a flow cell of a sequencing machine, within which millions of sequences are immobilized, amplified and sequenced. + 1.15 + + + + + + + + + + Run number + + 1.15 + A number corresponding to the number of an analysis performed by a sequencing machine. For example, if it's the 13th analysis, the run is 13. + + + + + + + + + + + Ecological data + + Data concerning ecology; for example measurements and reports from the study of interactions among organisms and their environment. + 1.15 + This is a broad data type and is used a placeholder for other, more specific types. + + + + + + + + + + Alpha diversity data + + α-diversity + The mean species diversity in sites or habitats at a local scale. + 1.15 + + + + + + + + + + Beta diversity data + + β-diversity + The ratio between regional and local species diversity. + True beta diversity + 1.15 + + + + + + + + + + Gamma diversity data + + The total species diversity in a landscape. + γ-diversity + 1.15 + + + + + + + + + + Ordination plot + + + A plot in which community data (e.g. species abundance data) is summarised. Similar species and samples are plotted close together, and dissimilar species and samples are plotted placed far apart. + 1.15 + + + + + + @@ -26526,8 +26653,8 @@ - Data model 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 @@ -28555,13 +28682,13 @@ - + - + Data format for the emission and transition counts of a hidden Markov model. @@ -28956,7 +29083,8 @@ OWL format - + + A serialisation format conforming to the Web Ontology Language (OWL) model. beta12orEarlier @@ -29250,11 +29378,10 @@ Textual format - http://filext.com/file-extension/TSV http://www.iana.org/assignments/media-types/text/plain Textual format. Data in text format can be compressed into binary format, or can be a value of an XML element or attribute. Markup formats are not considered textual (or more precisely, not plain-textual). - txt + txt http://filext.com/file-extension/TXT Plain text http://www.iana.org/assignments/media-types/media-types.xhtml#text @@ -29295,8 +29422,8 @@ beta12orEarlier eXtensible Markup Language (XML) format. xml - - Extensible Markup Language + + eXtensible Markup Language @@ -29376,19 +29503,19 @@ - + - + - + BioXSD XML format @@ -29396,6 +29523,8 @@ BioXSD XML format of basic bioinformatics types of data (sequence records, alignments, feature records, references to resources, and more). + + @@ -29406,12 +29535,17 @@ RDF format + Resource Description Framework format + RDF + Resource Description Framework + + - beta12orEarlier A serialisation format conforming to the Resource Description Framework (RDF) model. + @@ -29874,13 +30008,13 @@ - + - + Format of a bibliographic reference. @@ -30563,6 +30697,7 @@ GTrack is an optimised tabular format for genome/sequence feature tracks unifying the power of other tabular formats (e.g. GFF3, BED, WIG). + @@ -30904,10 +31039,8 @@ RDF/XML - - RDF Resource Description Framework (RDF) XML format. 1.2 http://www.ebi.ac.uk/SWO/data/SWO_3000006 @@ -31219,11 +31352,18 @@ JSON - + JavaScript Object Notation + + 1.7 - Javascript Object Notation format; a lightweight, text-based format to represent structured data using key-value pairs. + JavaScript Object Notation format; a lightweight, text-based format to represent tree-structured data using key-value pairs. + json + + + + @@ -31273,16 +31413,23 @@ TSV + Tab-separated values + Tabular format + Delimiter-separated values + DSV + Comma-separated values + CSV - Tabular format - http://filext.com/file-extension/CSV - http://www.iana.org/assignments/media-types/text/csv Tabular data represented as tab-separated values in a text file. 1.7 - http://filext.com/file-extension/TSV - CSV + tsv|tab + + + https://en.wikipedia.org/wiki/Delimiter-separated_values + http://filext.com/file-extension/CSV + http://www.iana.org/assignments/media-types/text/csv @@ -32442,6 +32589,7 @@ pepXML + http://sashimi.sourceforge.net/schema_revision/pepXML/pepXML_v118.xsd Open data format for the storage, exchange, and processing of peptide sequence assignments of MS/MS scans, intended to provide a common data output format for many different MS/MS search engines and subsequent peptide-level analyses. @@ -32476,11 +32624,10 @@ 1.12 oxlicg - http://www.iana.org/assignments/media-types/application/vnd.oxli.countgraph A list of k-mers and their occurences in a dataset. Can also be used as an implicit De Bruijn graph. - - + + @@ -32745,10 +32892,9 @@ experiments employing a combination of technologies. VDB - VDB ('vertical database') is the format (SRA) is the native format used for export from the NCBI Sequence Read Archive. + VDB ('vertical database') is the native format used for export from the NCBI Sequence Read Archive. SRA native format 1.13 - SRA @@ -32779,7 +32925,7 @@ experiments employing a combination of technologies. - sequin + Sequin format A five-column, tab-delimited table of feature locations and qualifiers for importing annotation into an existing Sequin submission (an NCBI tool for submitting and updating GenBank entries). 1.13 @@ -32795,7 +32941,7 @@ experiments employing a combination of technologies. MSF Magellan storage file format - This format corresponds to an SQLite database, and you can look into the files with e.g. SQLiteStudio3. There are also some readers (http://pubs.acs.org/doi/abs/10.1021/pr2005154) and converters (http://www.sciencedirect.com/science/article/pii/S1874391915300531) for this format available, which re-engineered the database schema, but there is no official DB schema specification of Thermo Scientific for the format. + This format corresponds to an SQLite database, and you can look into the files with e.g. SQLiteStudio3. There are also some readers (http://doi.org/10.1021/pr2005154) and converters (http://doi.org/10.1016/j.jprot.2015.06.015) for this format available, which re-engineered the database schema, but there is no official DB schema specification of Thermo Scientific for the format. Proprietary mass-spectrometry format of Thermo Scientific's ProteomeDiscoverer software. 1.14 @@ -32931,7 +33077,7 @@ experiments employing a combination of technologies. 1.14 MaxQuant APL Format of peak list files from Andromeda search engine (MaxQuant) that consist of arbitrarily many spectra. - + @@ -33016,6 +33162,101 @@ experiments employing a combination of technologies. + + + + BIOM format + BIological Observation Matrix format + + + The BIological Observation Matrix (BIOM) is a format for representing biological sample by observation contingency tables in broad areas of comparative omics. The primary use of this format is to represent OTU tables and metagenome tables. + BIOM is a recognized standard for the Earth Microbiome Project, and is a project supported by Genomics Standards Consortium. Supported in QIIME, Mothur, MEGAN, etc. + 1.15 + + + + + biom + + + + + + + + protXML + + + A format for storage, exchange, and processing of protein identifications created from ms/ms-derived peptide sequence data. + No human-consumable information about this format is available (see http://tools.proteomecenter.org/wiki/index.php?title=Formats:protXML). + 1.15 + + + + + + + + + + + + Linked data format + Linked Data format + Semantic Web format + + A linked data format enables publishing structured data as linked data (Linked Data), so that the data can be interlinked and become more useful through semantic queries. + 1.15 + + + + + + + + + + + + + JSON-LD + JavaScript Object Notation for Linked Data + + + + JSON-LD, or JavaScript Object Notation for Linked Data, is a method of encoding Linked Data using JSON. + 1.15 + + + + jsonld + + + + + + + + + + + YAML + YAML Ain't Markup Language + + YAML (YAML Ain't Markup Language) is a human-readable tree-structured data serialization language. + Data in YAML format can be serialised into text, or binary format. + YAML version 1.2 is a superset of JSON; prior versions were "not strictly compatible". + 1.15 + + + + yaml|yml + + + + + + @@ -33065,8 +33306,8 @@ experiments employing a combination of technologies. - Computational tool Computational tool provides one or more operations. + Computational tool @@ -33086,14 +33327,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -33232,9 +33473,13 @@ experiments employing a combination of technologies. Sequence merging + Read stitching beta12orEarlier + Paired-end stitching Merge two or more (typically overlapping) molecular sequences. + Paired-end merging Sequence splicing + Read merging @@ -33423,14 +33668,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -33480,14 +33725,14 @@ 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. @@ -33740,14 +33985,14 @@ experiments employing a combination of technologies. - - + + - - + + @@ -34044,14 +34289,14 @@ 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. @@ -34100,14 +34345,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -34244,14 +34489,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -34305,7 +34550,7 @@ experiments employing a combination of technologies. - + @@ -34317,20 +34562,20 @@ experiments employing a combination of technologies. - - + + - - + + - - + + beta12orEarlier @@ -34390,14 +34635,14 @@ experiments employing a combination of technologies. - - + + - - + + Sequence distance matrix construction @@ -34550,14 +34795,14 @@ experiments employing a combination of technologies. - - + + - - + + Sequence profile construction @@ -34577,8 +34822,8 @@ experiments employing a combination of technologies. - - + + @@ -34589,8 +34834,8 @@ experiments employing a combination of technologies. - - + + Structural profile generation @@ -34610,20 +34855,20 @@ experiments employing a combination of technologies. - - + + - - + + - - + + Sequence profile alignment @@ -34645,14 +34890,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -34811,14 +35056,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -34836,14 +35081,14 @@ experiments employing a combination of technologies. - - + + - - + + @@ -34887,14 +35132,14 @@ experiments employing a combination of technologies. - - + + - - + + @@ -34928,26 +35173,26 @@ experiments employing a combination of technologies. - - + + - - + + - - + + - - + + Predict and/or optimize oligonucleotide probes for DNA microarrays, for example for transcription profiling of genes, or for genomes and gene families. @@ -34967,14 +35212,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -35060,12 +35305,15 @@ experiments employing a combination of technologies. + Metagenomic inference Expression profiling + The measurement of the expression of multiple genes in a cell, tissue, sample etc., in order to get an impression of biological function. Gene expression profile construction Functional profiling - Generate a gene expression profile or pattern, for example from microarray data. beta12orEarlier Gene expression profile generation + Metagenomic inference is the profiling of phylogenetic marker genes in order to predict metagenome function. + Gene expression profiling generates some sort of gene expression profile or pattern, for example from microarray data. @@ -35248,14 +35496,14 @@ 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. @@ -35399,13 +35647,13 @@ experiments employing a combination of technologies. - + - + Protein SNP mapping @@ -35442,14 +35690,14 @@ experiments employing a combination of technologies. - - + + - - + + Predict and optimise zinc finger protein domains for DNA/RNA binding (for example for transcription factors and nucleases). @@ -35467,14 +35715,14 @@ experiments employing a combination of technologies. - - + + - - + + beta12orEarlier @@ -35524,8 +35772,8 @@ experiments employing a combination of technologies. - - + + @@ -35536,8 +35784,8 @@ experiments employing a combination of technologies. - - + + Visualization @@ -35924,13 +36172,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - + - + @@ -36512,14 +36760,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Calculate pH-dependent properties from pKa calculations of a protein sequence. @@ -36780,14 +37028,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Sequence feature detection (nucleic acid) @@ -37877,14 +38125,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + beta12orEarlier @@ -38041,7 +38289,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Dotplot plotting - + @@ -38283,14 +38531,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + RNA secondary structure alignment generation @@ -38793,7 +39041,6 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Gene expression profile analysis true - Functional profiling beta12orEarlier Analyse one or more gene expression profiles, typically to interpret them in functional terms. 1.6 @@ -39092,14 +39339,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Identify a plausible model of DNA substitution that explains a molecular (DNA or protein) sequence alignment. @@ -39146,14 +39393,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Predict families of genes and gene function based on their position in a phylogenetic tree. @@ -39328,18 +39575,19 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + + Visualise, format or render a molecular sequence or sequences such as a sequence alignment, possibly with sequence features or properties shown. beta12orEarlier - Visualise, format or render a molecular sequence, possibly with sequence features or properties shown. + Sequence alignment visualisation Sequence rendering @@ -39351,25 +39599,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Sequence alignment visualisation - - - - - - - - - - - - - - - Sequence alignment rendering + + 1.15 + true Visualise, format or print a molecular sequence alignment. beta12orEarlier - - + + @@ -39419,19 +39655,13 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern RNA secondary structure visualisation - - - - - - - - - RNA secondary structure rendering + + true + 1.15 Visualise RNA secondary structure, knots, pseudoknots etc. beta12orEarlier - - + + @@ -39439,19 +39669,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Protein secondary structure rendering Protein secondary structure visualisation - - - - - - - + Render and visualise protein secondary structure. beta12orEarlier - - + true + 1.15 + + @@ -39474,9 +39699,11 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - Structure rendering - Visualise or render a molecular tertiary structure, for example a high-quality static picture or animation. beta12orEarlier + Visualise or render molecular structure, for example a high-quality static picture or animation. This includes secondary structure such as knots, pseudoknots etc. as well as tertiary and quaternary structure. + Structure rendering + RNA secondary structure visualisation + Protein secondary structure visualisation @@ -39738,7 +39965,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - + beta12orEarlier @@ -40565,7 +40792,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Transmembrane protein visualisation - + @@ -40697,14 +40924,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Structure analysis (protein) @@ -40754,7 +40981,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - + beta12orEarlier @@ -40860,14 +41087,14 @@ 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. @@ -40887,14 +41114,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Analyse known protein secondary structure data. @@ -41213,7 +41440,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - + Predict a network of gene regulation. @@ -41410,14 +41637,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Compare two or more molecular sequences. @@ -41476,6 +41703,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Gene component prediction + Gene calling Detect, predict and identify genes or components of genes in DNA sequences, including promoters, coding regions, splice sites, etc. Whole gene prediction Gene and gene component prediction @@ -41614,14 +41842,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Identify or predict protein-protein interactions, interfaces, binding sites etc. @@ -41812,19 +42040,19 @@ 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. @@ -41910,14 +42138,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + Analyse nucleic acid tertiary structural data. @@ -41967,7 +42195,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Helical wheel drawing - + @@ -41987,7 +42215,7 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern Topology diagram drawing - + @@ -42603,14 +42831,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + beta12orEarlier @@ -42908,14 +43136,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + beta12orEarlier @@ -43008,14 +43236,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + beta12orEarlier @@ -43478,14 +43706,14 @@ sequences matching a given sequence motif or pattern, such as a Prosite pattern - - + + - - + + @@ -44138,11 +44366,13 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - Differential expression analysis - - Identify (typically from analysis of microarray or RNA-seq data) genes whose expression levels are significantly different between two sample groups. + Differential gene expression analysis + + Differentially expressed gene identification - 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. + Differential gene analysis + Differential gene 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. + Identify from molecular sequence analysis (typically from analysis of microarray or RNA-seq data) genes whose expression levels are significantly different between two sample groups. 1.1 @@ -44369,13 +44599,13 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - + - + @@ -44494,14 +44724,14 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - - + + - - + + Generate a checksum of a molecular sequence. @@ -44553,13 +44783,13 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - + - + 1.4 @@ -44604,14 +44834,14 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - - + + - - + + Recognition of which format the given data is in. @@ -45483,12 +45713,6 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - - - - - - @@ -45499,6 +45723,12 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp + + + + + + 1.12 Identify semantic relationships within a text or between two or more texts using text mining techniques. @@ -45613,14 +45843,14 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - - + + - - + + 1.12 @@ -46113,6 +46343,87 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp + + + + Cross-assembly + + 1.15 + Construction of a single sequence assembly of all reads from different samples, typically as part of a comparative metagenomic analysis. + Sequence assembly (cross-assembly) + + + + + + + + + + Sample comparison + + 1.15 + The comparison of samples from a metagenomics study, for example, by comparison of metagenome shotgun reads or assembled contig sequences, by comparison of functional profiles, or some other method. + + + + + + + Differential protein expression analysis + + + Differential protein analysis + 1.15 + The analysis, using proteomics techniques, to identify proteins whose encoding genes are differentially expressed under a given experimental setup. + + + + + + + + + + Differential expression analysis + + The analysis, using any of diverse techniques, to identify genes that are differentially expressed under a given experimental setup. + 1.15 + + + + + + + + + + Multiple sample visualisation + + Visualise, format or render data arising from an analysis of multiple samples from a metagenomics/community experiment. + 1.15 + + + + + + + + + + Ancestral reconstruction + + 1.15 + Ancestral reconstruction is often used to recover possible ancestral character states of ancient, extinct organisms. + The extrapolation of empirical characteristics of individuals or populations, backwards in time, to their common ancestors. + Character mapping + Character optimization + + + + + + @@ -46138,11 +46449,10 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - Nucleic acid analysis + Nucleic acids The processing and analysis of nucleic acid sequence, structural and other data. Nucleic acid bioinformatics - Nucleic acids Nucleic acid informatics http://purl.bioontology.org/ontology/MSH/D017423 Nucleic acid properties @@ -46159,16 +46469,15 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp - Protein analysis + Proteins - Protein informatics - Proteins - http://purl.bioontology.org/ontology/MSH/D020539 Protein bioinformatics + Protein informatics Protein databases true - beta12orEarlier + http://purl.bioontology.org/ontology/MSH/D020539 Archival, processing and analysis of protein data, typically molecular sequence and structural data. + beta12orEarlier @@ -46449,15 +46758,14 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Mapping + This includes 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. It also includes resources for physical (sequence) maps 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. It also covers for example the alignment of sequences of (typically millions) of short reads to a reference genome. + beta12orEarlier The mapping of complete (typically nucleotide) sequences. Mapping (in the sense of short read alignment, or more generally, just alignment) has application in RNA-Seq analysis (mapping of transcriptomics reads), variant discovery (e.g. mapping of exome capture), and re-sequencing (mapping of WGS reads). Genetic linkage Linkage Linkage mapping - true Synteny - This includes 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. It also includes resources for physical (sequence) maps 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. It also covers for example the alignment of sequences of (typically millions) of short reads to a reference genome. - DNA mapping - beta12orEarlier + true @@ -46582,12 +46890,14 @@ Trim sequences (typically from an automated DNA sequencer) to remove sequence-sp Proteomics beta12orEarlier + Metaproteomics Protein and peptide identification, especially in the study of whole proteomes of organisms. Protein and peptide identification Peptide identification Proteomics includes any methods (especially high-throughput) that separate, characterize and identify expressed proteins such as mass spectrometry, two-dimensional gel electrophoresis and protein microarrays, as well as in-silico methods that perform proteolytic or mass calculations on a protein sequence and other analyses of protein expression data, for example in different cells or tissues. true http://purl.bioontology.org/ontology/MSH/D040901 + Includes metaproteomics: proteomics analysis of an environmental sample. Protein expression @@ -47424,7 +47734,6 @@ long terminal repeats (LTRs); sequences (typically retroviral) directly repeated http://edamontology.org/topic_0197 Gene expression levels are analysed by identifying, quantifying or comparing mRNA transcripts, for example using microarrays, RNA-seq, northern blots, gene-indexed expression profiles etc. http://purl.bioontology.org/ontology/MSH/D015870 - Gene expression analysis DNA microarrays The analysis of levels and patterns of synthesis of gene products (proteins and functional RNA) including interpretation in functional terms of gene expression data. Codon usage @@ -49034,7 +49343,7 @@ positional features such as functional sites in nucleotide sequences. - Prokaryotes and archae + Prokaryotes and Archaea The resource may be specific to a prokaryote, a group of prokaryotes or all prokaryotes. VT 1.5.2 Bacteriology @@ -50213,7 +50522,6 @@ positional features such as functional sites in nucleotide sequences.The development and use of architectures, policies, practices and procedures for management of data. true beta13 - Data handling http://purl.bioontology.org/ontology/MSH/D030541 VT 1.3.1 Data management @@ -50447,6 +50755,7 @@ positional features such as functional sites in nucleotide sequences. Sequencing + Amplicon sequencing is the ultra-deep sequencing of PCR products (amplicons), usually for the purpose of efficient genetic variant identification and characterization in specific genomic regions. Resequencing true http://purl.bioontology.org/ontology/MSH/D059014 @@ -50456,9 +50765,11 @@ positional features such as functional sites in nucleotide sequences.DNA-Seq High throughput sequencing 1.1 + High-throughput sequencing Primer walking Next generation sequencing The determination of complete (typically nucleotide) sequences, including those of genomes (full genome sequencing, de novo sequencing and resequencing), amplicons and transcriptomes. + Amplicon sequencing @@ -50563,6 +50874,7 @@ positional features such as functional sites in nucleotide sequences.Environmental genomics true 1.1 + Shotgun metagenomics The study of genetic material recovered from environmental samples, and associated environmental data. @@ -50669,7 +50981,6 @@ positional features such as functional sites in nucleotide sequences.Sample collections samples - biobanking 1.3 biosamples Biological samples and specimens. @@ -50688,7 +50999,6 @@ positional features such as functional sites in nucleotide sequences. VT 1.5.4 Biochemistry and molecular biology - Chemical biology 1.3 Biological chemistry true @@ -50804,7 +51114,7 @@ positional features such as functional sites in nucleotide sequences. Microbiology - + true The biology of microorganisms. 1.3 @@ -51418,7 +51728,6 @@ positional features such as functional sites in nucleotide sequences.Biomaterials Any matter, surface or construct that interacts with a biological system. - Diagnostic markers 1.4 @@ -51848,7 +52157,6 @@ positional features such as functional sites in nucleotide sequences. 1.4 The application of biological concepts and methods to the analytical and synthetic methodologies of engineering. - Diagnostic markers @@ -52167,12 +52475,11 @@ positional features such as functional sites in nucleotide sequences. Opthalmology - Eye disoders - VT 3.2.18 Optometry - 1.4 Optometry + 1.4 + Eye disoders VT 3.2.17 Ophthalmology - Audiovestibular medicine + VT 3.2.18 Optometry The branch of medicine that deals with disorders of the eye, including eyelid, optic nerve/visual pathways and occular muscles. @@ -52220,7 +52527,6 @@ positional features such as functional sites in nucleotide sequences.Reproductive health Reproductive disorders - Audiovestibular medicine VT 3.2.3 Andrology Andrology 1.4 @@ -52992,7 +53298,6 @@ positional features such as functional sites in nucleotide sequences. Data governance - Data handling http://purl.bioontology.org/ontology/MSH/D030541 The control of data entry and maintenance to ensure the data meets defined standards, qualities or constraints. 1.10 @@ -53164,9 +53469,8 @@ positional features such as functional sites in nucleotide sequences.Exome capture Exome sequencing is considered a cheap alternative to whole genome sequencing. Targeted exome capture - Exome sequence analysis - Laboratory technique to sequence all the protein-coding regions in a genome, i.e., the exome. Exome analysis + Laboratory technique to sequence all the protein-coding regions in a genome, i.e., the exome.