EDAM 1.25

See the changelog-detailed.md for a detailed list of semantic changes in the EDAM ontology.

• Addition of new concepts, and other improvements (synonyms, hierarchy) for human copy number variation analysis.
• Addition of new format concepts in support of GigaScience database, GigaDB.
• Addition of misc. new concepts requested via the tracker
• Dozens of new synonyms in the EDAM Topic subontology mostly.
• Clean-up of Expression analysis including undeprecation of Gene expression profiling (now child of Expression analysis), clean-up of synonyms, hiearchy improvements etc. clarifying the concepts.
• Addition of links to Wikipedia

Changes in hierarchy

• 52 concepts added (5 Topic, 9 Operation, 0 Data, 38 Format)
• 7 concept relations changed (0 Topic, 6 Operation, 0 Data, 1 Format, 1 undeprecated)
• 0 concepts deprecated

Fixed issues

• 30 "concept or term request" issues fixed and closed (see milestone 1.25)
• 2 enhacements (#525, #527)
• 1 bug fixed (#524)

EDAM 1.24 release

See the changelog-detailed.md for a detailed list of semantic changes in the EDAM ontology.

• revisions following mapping and gap analysis of EDAM to keywords used by IFB for tagging their resources, including IFB tools
• revision of existing synonyms and addition of new ones
• revision of concept preferred labels (which now better reflect the vernacular)
• consolidation of some overlapping concepts
• cleaned-up mixed notions of "pathway" and "network" (now neatly organised under Network analysis and Pathway analysis

Changes in hierarchy

• 39 concepts added
• 8 concepts deprecated

Fixed issues

• 95 "concept or term request" issues fixed and closed (#419, #422 - #426, #429 - #449, #451 - #465, #466 - #501, #503 - #509, #511 - #517)
• 1 issue partially fixed (#502)
• 2 issues won't fix (#450, #466)
• 6 bugs fixed (#427, #428, #434, 506, #508, 518)

EDAM 1.21

See the improved changelog-detailed.md for a detailed list of semantic changes in the EDAM ontology.

Summary of changes

• 20 formats added (listed in changelog-detailed.md)
• Added repository attribute for Formats
• Structural clean-up of various areas of the Data sub-ontology, especially around Identifier and Report
• Major clean-up of the hierarchy of Accessions
• Clean-up of some Operations (e.g. around Plotting i.e. Visualisation)
• Major improvements of the EDAM documentation
• Improved edam2json generator

Changes in hierarchy

• 26 concepts added (3 Data, 20 Format, 2 Operation, 1 Topic)
• 13 concepts deprecated (11 Data, 2 Operation)
• 315 concepts have changed relations|hierarchy (297 Data, of which 282 Identifier; 9 Format, 9 Operation)

Fixed issues

• 25 issues fixed and closed (#67, #190, #206, #233, #244, #253, #271, #288, #338, #339, #340, #341, #342, #343, #344, #345, #347, #348, #349, #351, #364, edamontology/edamontologyDocs#1, edamontology/edamontologyDocs#18, edamontology/edam2json#1, edamontology/edam2json#2)
• 4 issues partially fixed but left open for further improvements (#15, #237, #293, #295)

Other closed issues

• 0 invalid issues closed ()
• 5 issues closed, wrong project (#174, #299, #334, #354, #355)
• 0 issues closed, won't fix ()
• 2 issues closed, duplicate (#291, #322)

EDAM 1.20

See the improved changelog-detailed.md for the detailed list of semantic changes in the EDAM ontology.

Summary of changes

• Numerous Formats added (27, listed in changelog-detailed.md)
• Added Topics Agricultural Science and Metagenomic sequencing
• Improved a number of synonyms and labels (especially among Operations and Topics)
• Fixed a couple of bugs in syntax and subset
• Binary format defined as strictly disjoint with HTML, XML, and Textual format
• Pre-parsing EDAM into "unrolled" JSON tree structure by edam2json (#326)
• Additional CI validations by edamxpathvalidator: label, definition, consider, replacedBy
• Added a browsable latest-stable version of EDAM to WebProtégé as EDAM latest stable permalink
• Major improvements of the changelog-detailed.md file listing detailed semantic changes between stable versions of EDAM

Changes in hierarchy

• 29 concepts added (27 Format, 2 Topic)
• 7 concepts deprecated (3 Data, 1 Format, 3 Operation)
• 7 concepts have changed relations|hierarchy (3 Format, 4 Operation)

Fixed issues

• 22 issues fixed and closed (#122, #143, #183, #197, #198, #199, #200, #211, #234, #261, #262, #272, #285, #286, #304, #327, #329, #330, #331, #332, #333, #337)
• 5 issues partially fixed but left open for further improvements (#128, #164, #265, #271, #326)

Other closed issues

• 1 invalid issue closed (#176)
• 0 issues closed, wrong project ()
• 3 issues closed, won't fix (#69, #219, #296)
• 4 issues closed, duplicate (#128, #166, #193, #297)

EDAM 1.19

Summary of changes

• Various deprecations, synonyms, and rearrangements in the Operation sub-ontology
• Clean-up of technical artifacts: most newlines and all tab characters removed (from definitions etc.), corrections of wrong created_in-s, corrections of deprecated concepts (subset-s, relations, replacement concepts, etc.)
• Clean-up of the git repo
• Changes and additions of concepts related to electron microscopy
• Other updates (e.g. among Identifiers and Formats)

Changes in hierarchy

• 5 concepts added (4 Data, 1 Operation)
• 28 concepts deprecated (1 Data, 27 Operation)
• 71 concepts have changed relations|hierarchy (1 Data, 70 Operation)

See changelog-detailed.md for the list of additions, deprecations, and changes in relations between concepts.

Fixed issues

• 22 issues fixed and closed (#266, #267, #277, #300, #301, #303, #304, #307, #308, #309, #310, #311, #312, #313, #314, #315, #316, #317, #318, #320, #323, #324)
• 2 issues partially fixed but left open for further improvements (#257, #268)

Other closed issues

• 4 invalid issues closed (#208, #209 #298, #325)
• 0 issues closed, wrong project ()
• 0 issues closed, won't fix ()
• 3 issues closed, duplicate (#205, #212, #320)

EDAM 1.18

EDAM_1.18.owl

See changelog-detailed.md for additions, deprecations, and changes in relations between concepts.

EDAM_1.18 includes:

• EDAM is now available in 2 additional formats: CSV and TSV
  • http://edamontology.org/EDAM.csv is optimised for use in spreadsheet apps (e.g. Excel)
  • http://edamontology.org/EDAM.tsv is optimised for scripting
  • Available for EDAM versions 1.16 and newer
  • More details in #268
• EDAM versions are now graphically browsable online in WebProtégé
  • Free registration required
  • Available for EDAM versions 1.16 and newer, including the unstable development version
  • Links to the different EDAM versions are at http://edamontology.org/page#Viewing and in README.md
• EDAM releases now have DOIs
  • DOI representing all released versions, resolving to the latest: 10.5281/zenodo.822690
  • DOI of EDAM version 1.18: 10.5281/zenodo.822691
• various refactoring including concepts deprecations within the Operation sub-ontology to make this simpler and improve usability
• new attribute to provide tips e.g. in bio.tools UI indicating "organisational concepts", i.e. higher-level concepts which primarily structure the hierarchy and are not normally recommended for annotation
• LICENSE added to the EDAM repo (in .md and plain text) for immediate recognition

Changed

• 37 concepts have changed place in the hierarchy (37 Operation)

Deprecated

• 16 concepts deprecated (16 Operation)

Fixed

• 6 issues fixed and closed (#269, #270, #273, #275, #276, #280)
• 3 issues partially fixed but left open for further improvements (#265, #268, #277)

Misc

• 0 invalid issues closed ()
• 0 issues closed, wrong project ()
• 1 issue closed, won't fix (#264)
• 0 issues closed, duplicate ()
• 0 issues reopened ()

EDAM 1.17

EDAM_1.17.owl

See the detailed change log for additions, deprecations, and changes in relations between concepts.

EDAM_1.17 includes:

• addition of concepts for sequencing terms from SEQWiki
• addition of Spectral library search
• miscellaneous term requests, bug fixes and other changes received via GitHub
• deprecation of multiple Topics (especially removing organism types from under Model organisms), and Operations
• simplification to Operation branch for sequence feature detection concepts
• new attributes for better provenance on deprecated concepts
  • oldParent: attribute for URI of erstwhile parents of now deprecated concepts
  • deprecation_comment: comment as to why the concept was deprecated
• multiple typo and other minor fixes

Added

• 14 concepts added (11 Operation, 2 Topic, 1 Format)

Changed

• 24 concepts changed (20 Operation, 4 Topic; minor edits or relational|synonym changes)

Deprecated

• 15 concepts deprecated (8 Topic, 7 Operation)

Fixed

• 15 issues fixed and closed (#118, #241, #243, #247, #248, #250, #251, #252, #254, #255, #256, #258, #259, #260, edamontology/edamxpathvalidator#4)
• 2 issues partially fixed but left open for further improvements (#128, #268)

Misc

• 1 invalid issue closed (#203)
• 1 issue closed, wrong project (#240)
• 1 issue closed, won't fix (#185)
• 2 issues closed, duplicate (#242 fixed in #241, #249 fixed in #118)
• 2 issues reopened (#118 fixed, #130)

EDAM 1.16

See the detailed change log for exact details of changes.

EDAM_1.16 includes:

• concept and term updates and additions, as requested by EDAM users (mostly Bio.Tools registrants), including ones for text mining and natural language processing (BioNLP), and gene expression
• structural improvements and fixes, improvements of synonyms, new attributes for formats

Added

• 40 concepts added (23 Format, 9 Data, 8 Operation)

Changed

• 32 concepts changed relations (12 Data, 12 Operation, 7 Format, 1 Topic)
• Added synonyms, updated primary terms and synonyms of various concepts
• Added Wikipedia links to some concepts
• Added documentation, examples, citations, media types, file extensions, information standards, organisations, and used ontologies of a couple of Format concepts

Deprecated

• 7 concepts deprecated (6 Operation, 1 Data)

Fixed

• 32 issues fixed and closed (#99, #139, #177, #178, #179, #180, #181, #182, #186, #187, #188, #189, #191, #192, #194, #195, #196, #201, #202, #217, #220, #221, #222, #223, #224, #225, #227, #228, #230, #231, #232, #238)
• 4 issues partially fixed but left open for further improvements (#6, #120, #143, #237)

Misc

• 0 invalid issues closed ()
• 4 issues closed, wrong project (#161, #170, #192, #229)
• 1 issue closed, won't fix (#226)
• 3 issues closed, duplicate (#126, #167, #175)

EDAM 1.15

See the detailed change log for exact details of changes.

EDAM_1.15 includes:

• new concepts and terms requested by the community, including ones for environmental omics and biodiversity
• structural improvements and fixes, including a clean-up of synonyms (automation of this in the pipeline), updates of formats, and simplification of Visualisation concepts

Added

• 20 concepts added (9 Data, 6 Operation, 5 Format)

Changed

• 24 concepts changed (9 Data, 5 Format, 9 Operation, 1 Topic)
• Added citations, media types, and/or file extensions of some Format concepts
• Added and/or cleaned-up synonyms of various concepts

Deprecated

• 5 concepts deprecated (2 Data, 3 Operation)

Fixed

• 26 issues fixed and closed (#119, #121, #130, #131, #132, #133, #134, #135, #136, #141, #142, #144, #145, #146, #150, #151, #152, #156, #157, #158, #159, #160, #165, #168, #169, #172)
• 3 issues fixed and left open for eventual further discussion (#120, #143, #166)

Misc

• 1 invalid issue closed (#149)
• 2 issues closed, wrong project (#153, #154)
• 4 issues closed, won't fix (#125, #147, #148, #155)
• 2 other issues closed (#124, #140)

EDAM 1.14

EDAM_1.14.owl

See the detailed change log for exact details of changes.

EDAM_14 includes:

• many new terms or term corrections requested by the community (directly on github, or during the last hackathons).
• a new CI process that will be extended over time to monitor and improve the quality of the ontology.

Added

• 14 classes changed

Changed

• 28 classes added, mainly new data and formats.