EDAM Ontology

EDAM README See http://edamontology.net/ // EDAM_1.2.obo This is the first version of EDAM now that is maintained in OWL format. The OBO-format version is generated from it by processing the OWL file. Highlights of changes: * New references to Wikipedia * New synonyms * New equivalence statements (mostly on high-level EDAM concepts) to concepts in other ontologies * About a dozen new formats * New references to external ontologies (i.e. mostly on lower-level EDAM concepts) defining boundaries to other ontologies (work in progress!) * Clean-ups for cleaner viewing in Protege and OLS: * Removed unnecessary has_input, has_output axioms * Cleaner annotations on the ontology itself // EDAM_1.1.obo Many additions (mostly in "Operation" and some in "Topic" branches) for "next generation" sequencing analysis. EDAM now provides complete coverage of biological domains and bioinformatics methods from SeqWiki (http://seqanswers.com/wiki/SEQanswers) SeqWiki "biological domains" map to EDAM "Topic", SeqWiki "bioinformatics methods" map to EDAM "Operation" // EDAM_1.0.obo The first release proper. General changes * New style for concept IDs: 4 digit number, subontology namespace / subset("operation", "topic" etc) e.g. "EDAM_operation:0004" (new style) instead of "EDAM:0000004" (old style) * New relations (has_function, is_function_of) are defined for use by annotators (they are not used in EDAM itself) * Synonyms are defined that define related or relevant concepts in many other ontologies and systems. Synonyms are added throughout but especially on top-level concepts (Operation, Data, Format and Topic) and relations (has_input, is_input_of, has_output, is_output_of, has_topic, is_topic_of, has_format, is_format_of, has_function, is_function_of) * New concept attributes and modifiers have been added, most importantly: "{note} for comments on synonyms and other attributes, e.g. synonym: "assembly" NARROW [SO:0001248] {note="Perhaps surprisingly, the definition of 'SO:assembly' is narrower than the 'SO:sequence_assembly'."} "{since} for annotation of version information, e.g. data of creation or obsoletion of a concept id: id: EDAM_data:3165 {since=1.0} is_obsolete: true {since=1.0} "Format" branch * 10 new formats // EDAM_beta13.obo General changes * "Identifier" branch moved from top-level to beneath "Data". The "identifier" namespace / definitions have been kept! * Extensive revision of "Data", "Operation" and "Topic" branches to reduce clutter and ease navigation. * Bottom-up clean up removing terms that are too fine-grained. Top-down clean up to add or remove terms to aid navigation. * has_topic (defined on "Data" and "Operation") replaces in_topic * Duplicated relationships (child terms erroneously restating the inherited relationships of their parents) have been removed. "Data" branch * All "Data" concepts now organised into 4 sub-concepts: - "Core data" - Data that typically are the primary input or output of a tool or which correspond to entries from the primary (e.g. sequence or structural) biological databases. - "Identifier" - A short numerical or textual label that identifies (typically uniquely) something such as data, a resource or a biological entity. - "Parameter" - Typically a simple numerical or string value that controls the operation of a tool. - "Report" - A human-readable collection of information that is distinct from primary (e.g. sequence or structural) biological data, including free text, annotation about biological entities and phenomena, computer-generated reports of analysis of primary data and metadata. * "Report" concepts for sequences correspond better (without duplicating) established sequence feature keys. "Operation" branch * Fewer concepts, simpler is_a hierarchy * "has_input" and "has_input" relations defined (on nearly all terms) "Format" branch * "is_format_of" relations defined (for nearly all terms) "Topic" branch * Improved term names and is_a hierarchy, reflecting whether topics concern a type of data, operation or are more general. * New "Biological data resources" sub-branch includes common data resource concepts. * Major revision! Too much to mention, so take a look :) // EDAM_beta12.obo General changes * OBO subset definitions added * Sub-ontologies / namespaces / subsets now are "topic", "data", "format", "identifier", "operation" * Relation types now are "in_topic", "has_input", "has_output", "is_format_of", "is_identifier_of" * Many edits (to concepts and "is_a" relations) to improve navigability in all sub-ontologies New "Identifier" sub-ontology * Containing concepts which were under Data<-Identifier * For fine-grained annotation of identifiers of data (see http://edamontology.sourceforge.net/#9.6) "Resource" sub-ontology obsoleted * Most concepts merged into "Topic" sub-ontology (see below) * All remaining concepts in "resource" namespace obsoleted Major revisions to "Topic" sub-ontology * Concepts redefined as "...general bioinformatics subject or category, such as a field of study, data, processing, analysis or technology." * For coarse-grained annotation of diverse resources * Subsumes concepts from old "resource" sub-ontology (see above) EDAM-specific relations * Many new relations added (most term statements which should define relations now do) * Relations defined on parent only (not duplicated in children) "Format" sub-ontology * About 50 new formats added // EDAM_beta11.obo * Entire "Entity" branch (all terms) made obsolete * Root term of "resource" namespace ("Data resource") renamed to "Resource" * Root term of "format" namespace ("Data format") renamed to "Format" * Corrections (2) removing duplicate IDs // EDAM_beta10.obo Major revision of "Operation" branch * immensely simplified top level * better hierarchy Major revision of "Data" branch * simpler top-level * better hierarchy * new branches for "Protein data", "Nucleic acid data" * new terms to aid navigation * clean up "annotation" and "metadata" concepts Major revision of "Data format" branch * better hierarchy * children of "HTML format" are now (mostly) obsolete * many new formats added Simplification of "Topic" branch * concepts are now more strictly "fields of study" General changes * term relations are now defined in one direction only * more consistent usage of words in term names * more intuitive term names (child names follow parent in style where possible) * many term additions and deletions