EDAM_1.13.owl

See the detailed change log for exact details of changes.

22 new concepts were added and 1075 were changed.

Added

• multiple new formats and operations added, following requests from de.nbi and EBI hackathons

Modified

• multiple references to obsolete concepts to point to their replacements (consider and replacedBy)
• addition of the mapping to debtags, following the Debian-Med sprint
• a few topics structure changes
• a few miscelaneous corrections

EDAM_1.12.owl

See the detailed change log for exact details of changes.

56 new concepts were added and 190 concepts changed.

Added

• 56 new concepts added
• new concepts for mass spec from analysis of msutils.org
• new concepts for NGS from analysis of SEQanswers Wiki
• misc. additions arising from the recent hackathons in Brno, CZ and Amsterdam, NL
• multiple new synonyms

Changed

• reorganisation of top-level Operation concepts to make this branch more usable
• reorganisation of top-level Data concepts to make this branch more usable

Deprecated

• 72 concepts were deprecated
• removal of overly-specific Topic concepts that were overlapping with operations
• removal of overly-specific Data and Operation concepts
• removal of some obscure organisational classes (e.g. <Operation (typed)>)

Added

• 44 new formats have been added, based on the needs of the Galaxy (http://usegalaxy.org), ReGaTE (https://github.com/bioinfo-center-pasteur-fr/ReGaTE), and Common Workflow Language (https://github.com/common-workflow-language) projects, as part of the BOSC Codefest 2015 (http://open-bio.org/wiki/Codefest-2015.html).

Added

• hasDBXref class annotations added to Topic concepts to provide mapping to all VT Scientific Disciplines in branches 1.1 Mathematics, 1.2 Computer sciences, 1.3 Information sciences, 1.5 Biological sciences, 1.7 Chemical sciences, 3. Medical and Health Sciences, 3.2 Clinical medicine, 3.3 Health sciences and 3.4 Medical biotechnology.
• 9 new Topic concepts from mapping to VT Scientific Disciplines.
• 3 new Format concepts and 2 new Data concepts.

Changed

• 'Topic:Informatics' undeprecated and used as placeholder for various information science-related terms.
• 'Topic:Data management' and 'Topic:Computer science" siblings rearranged for conceptual clarity.

Fixed

• Multiple duplications of synonyms and labels in Topics branch.

Misc

Style of Topic concept definitions changed, removing "Topic concerning ...", to make them more usable.

Citing changelog.md, EDAM 1.9 includes:

• 20 new concepts in preparation for the ELIXIR Tools and Data Services Registry,
• 1 concept deprecation,
• Various minor changes (synonyms etc.).

Citing changelog.md, EDAM 1.8 includes:

• Revision to provide comprehensive coverage of EBI Tool Topics, Data and Operations
• Removal of fine-grained report (human-readable data) concepts from the Data branch
• Rooting all report concepts under "Data->Report"
• Removal of operation-like concepts from the Topics branch
• Biological concepts (sequence feature-related, pathways and networks, experimental techniques) that were previously modeled under as reports within Data, are now given under Topic
• Simplification of key Data concepts concerning sequences, alignments and signatures (motifs/profiles)
• Many other additions and minor changes
• 107 concept deprecations
• 53 new concepts

Citing changelog.md, EDAM 1.7 includes:

• Additions and changes following from the recent ELIXIR Registry Hackathon (tinyurl.com/RegistryHackathon).

• About 50 new concepts added

• 9 concept deprecations

• Many minor changes (new synonyms, minor structural changes etc.)

  Bug fixes

• Fixed synonyms that had URIs as values (1)

(1) for any synonyms that had a URI as value, that URI is now given as a seeAlso annotation instead. It was also necessary to remove all owl:annotatedProperty statements that defined a synyonm, from all "annotations on annotations", i.e. where comments had been added to an annotation on a class, via an owl:Axiom statement.

Citing changelog.md, EDAM 1.6 includes:

• A major revision of the EDAM Operation branch to simplify it and improve usability.
• 64 EDAM Operation concept deprecations.
• Top-level Operations now correspond to tool types in the ELIXIR Tools & Data Services Registry: Analysis, Query and retrieval, Visualisation, Deposition, Utility operation.
• Removal of excessively fine-grained Operation concepts.
• Removal of unnecessary "organisational" classes.
• Renaming of concepts (terms) to reflect the common terms in use.

Citing changelog.md, EDAM 1.5 includes:

• A major revision of the EDAM Data branch aiming for simplification and ease of use.

• 117 EDAM Data concept deprecations

• simplification of Data hierarchy

• removal of excessively fine-grained Dat concepts

• removal of out-of-scope Data concepts

• removal of unnecessary "organisational" classes (near top of Data hierarchy)

• renaming of concepts (terms) to reflect the common terms in use

• addition of Data synonyms

  Bug fixes

• fixed many references to deprecated concepts

Citing changelog.md, EDAM 1.4 includes:

• A major revision of the "Topic" sub-ontology expanding this into medical concepts (~60 new topics), following an effort led by Cath Brooksbank with major input from partners from EMTRAIN (European Medicines research TRAINing network) and partners from related ESFRI (European Strategy Forum on Research Infrastructures) projects.

• Fixing many minor bugs (mostly overlapping or bad synonyms) within topics, and other clean-ups.

• Removed the lowest tier of the "Topic" branch (mostly by moving terms up a level).

• Removed all oboOther:namespace and some subsets; removed most oboInOwl:inSubset for deprecated concepts and added subset 'obsolete'.

• New forms of UniProt identifiers added (regex).

• Examples of IANA and chemical media types added.

• A couple of file-/data-handling concepts added (operations and an identifier).

• An OBO-format version of EDAM has been omitted. We will only resume providing OBO format in case of substantial demand or full automation of the conversion.

• Documentation files have been substantially updated, e.g. specifying channels for the most welcome community contributions.

  And most importantly:

• EDAM is now being developed at GitHub!!!