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Added terms for formats for BioSimulators #766

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@jonrkarr jonrkarr commented Sep 21, 2021

(Restarts PR #729 previously approved by @veitveit which I unintentionally closed by renaming the associated branch. The PR is now merged with EDAM:main as of 9/21/2021.)

This pull request adds several new format terms needed for biomodeling and biosimulation and makes several corrections to existing terms for related formats. We are providing this as a PR to incorporate these terms. We're starting to need these terms and want to avoid trying to work with a fork for EDAM with different identifiers that we'd eventually need to sync with EDAM.

jonrkarr and others added 28 commits June 18, 2021 11:46
…BML composite, SBML multi-state/multi-species, SBML groups, SBML dFBA, Dockerfile, BioSimulators simulator specifications, and BioSimulators standard for command-line interface
- Corrected encoding of media types for format_3951, format_3969, format_3970, format_3971, format_3972, format_3977
format_3972
- Added media types for format_2585, format_3506, format_3590, format_3620, format_3685, format_3686, format_3688, format_3909, format_3972, format_3977, format_4015
- Added extensions for format_2585, format_3506, format_3590, format_3620, format_3626, format_3685, format_3686, format_3688, format_3972, format_3977, format_4015
- Removed file extension from format_3973 -- Dockerfiles and Docker images are separate formats
- Updated publication for format_3909
- Added documentation links for format_3909
- Added publication for format_3951
- Changed documentation to citation for format_3969, format_3970, format_3971, format_3972
- Added citation for format_3977
- Added synonyms for format_3506, format_3620
- removed parent format_2571 of format_3973
- removed parent format_3166 of format_3239
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sonarcloud bot commented Sep 21, 2021

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
No Duplication information No Duplication information

@jonrkarr jonrkarr changed the title Added terms for Biosimulators Added terms for formats for BioSimulators Sep 21, 2021
@LucieLamothe LucieLamothe added the concept/term addition Request for a new concept(s), or change(s) to existing concept(s) label Sep 30, 2021
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jonrkarr commented Oct 6, 2021

@veitveit could use approve again?

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sonarcloud bot commented Nov 3, 2021

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
No Duplication information No Duplication information

@matuskalas matuskalas added this to the 1.26 milestone Dec 17, 2021
@matuskalas matuskalas self-assigned this Dec 17, 2021
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