mbrochhausen
commented
2 years ago I am grateful for this bug report and I will follow up with it ASAP.
However, from a motivational and psychological perspective not using the word "offenders" might prove helpful. Just my 2 cents...
Best, Mathias
On Wed, Nov 3, 2021 at 11:03 AM Charles Tapley Hoyt < @.***> wrote:
As a follow-up to #1635 https://github.com/OBOFoundry/OBOFoundry.github.io/pull/1635 and with some wisdom from Nico given in related issue #1636 https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1636, there are several conflicts between the license labels and license URLs. Most of these are due to the lack of specificity of the CC-BY version. Here's a table of all offenders, plus the actionable contact information on who is responsible for the ontology in case someone is inclined to nudge them: prefix license_label license_url contact email github tracker aism http://www.obofoundry.org/ontology/aism CC-BY https://creativecommons.org/licenses/by/4.0/ Jennifer C. Girón @. https://github.com/insect-morphology/aism amphx http://www.obofoundry.org/ontology/amphx CC-BY http://creativecommons.org/licenses/by/3.0/ Hector Escriva @. https://github.com/EBISPOT/amphx_ontology aro http://www.obofoundry.org/ontology/aro CC-BY https://creativecommons.org/licenses/by/4.0/ CARD @. @raphenya https://github.com/raphenya https://github.com/arpcard/aro bfo http://www.obofoundry.org/ontology/bfo CC-BY http://creativecommons.org/licenses/by/4.0/ Barry Smith @. @phismith https://github.com/phismith https://github.com/BFO-ontology/BFO bspo http://www.obofoundry.org/ontology/bspo CC-BY http://creativecommons.org/licenses/by/3.0/ Chris Mungall @. @cmungall https://github.com/cmungall https://github.com/obophenotype/biological-spatial-ontology cdno http://www.obofoundry.org/ontology/cdno CC-BY https://creativecommons.org/licenses/by/3.0/ Liliana Andres Hernandez @. @LilyAndres https://github.com/LilyAndres https://github.com/Southern-Cross-Plant-Science/cdno chmo http://www.obofoundry.org/ontology/chmo CC-BY http://creativecommons.org/licenses/by/4.0/ Colin Batchelor @. @batchelorc https://github.com/batchelorc https://github.com/rsc-ontologies/rsc-cmo cido http://www.obofoundry.org/ontology/cido CC-BY http://creativecommons.org/licenses/by/4.0/ Yongqun Oliver He @. https://github.com/cido-ontology/cido cl http://www.obofoundry.org/ontology/cl CC-BY http://creativecommons.org/licenses/by/4.0/ Alexander Diehl @. @addiehl https://github.com/addiehl https://github.com/obophenotype/cell-ontology clo http://www.obofoundry.org/ontology/clo CC-BY http://creativecommons.org/licenses/by/3.0/ Sirarat Sarntivijai @. https://github.com/CLO-Ontology/CLO clyh http://www.obofoundry.org/ontology/clyh CC-BY http://creativecommons.org/licenses/by/3.0/ Lucas Leclere @. @L-Leclere https://github.com/L-Leclere https://github.com/EBISPOT/clyh_ontology cro http://www.obofoundry.org/ontology/cro CC-BY https://creativecommons.org/licenses/by/2.0/ Marijane White @. @marijane https://github.com/marijane https://github.com/data2health/contributor-role-ontology cteno http://www.obofoundry.org/ontology/cteno CC-BY http://creativecommons.org/licenses/by/3.0/ Chris Mungall @. @cmungall https://github.com/cmungall https://github.com/obophenotype/ctenophore-ontology cto http://www.obofoundry.org/ontology/cto CC-BY http://creativecommons.org/licenses/by/4.0/ Dr. Alpha Tom Kodamullil @. @akodamullil https://github.com/akodamullil https://github.com/ClinicalTrialOntology/CTO dpo http://www.obofoundry.org/ontology/dpo CC-BY http://creativecommons.org/licenses/by/3.0/ Clare Pilgrim @. https://github.com/FlyBase/drosophila-phenotype-ontology dron http://www.obofoundry.org/ontology/dron CC-BY http://creativecommons.org/licenses/by/3.0/ William Hogan @. https://github.com/ufbmi/dron/ duo http://www.obofoundry.org/ontology/duo CC-BY http://creativecommons.org/licenses/by/4.0/ Melanie Courtot @. @mcourtot https://github.com/mcourtot https://github.com/EBISPOT/DUO ecao http://www.obofoundry.org/ontology/ecao CC-BY http://creativecommons.org/licenses/by/3.0/ Charles Ettensohn @. @ettensohn https://github.com/ettensohn https://github.com/echinoderm-ontology/ecao_ontology ecocore http://www.obofoundry.org/ontology/ecocore CC-BY http://creativecommons.org/licenses/by/3.0/ Pier Luigi Buttigieg @. @pbuttigieg https://github.com/pbuttigieg https://github.com/EcologicalSemantics/ecocore envo http://www.obofoundry.org/ontology/envo CC-BY http://creativecommons.org/licenses/by/3.0/ Pier Luigi Buttigieg @. @pbuttigieg https://github.com/pbuttigieg https://github.com/EnvironmentOntology/envo eupath http://www.obofoundry.org/ontology/eupath CC-BY http://creativecommons.org/licenses/by/4.0/ Chris Stoeckert @. @cstoeckert https://github.com/cstoeckert https://github.com/VEuPathDB-ontology/VEuPathDB-ontology fbbt http://www.obofoundry.org/ontology/fbbt CC-BY http://creativecommons.org/licenses/by/3.0/ Clare Pilgrim @. fbcv http://www.obofoundry.org/ontology/fbcv CC-BY http://creativecommons.org/licenses/by/3.0/ Clare Pilgrim @. https://github.com/FlyBase/flybase-controlled-vocabulary fbdv http://www.obofoundry.org/ontology/fbdv CC-BY http://creativecommons.org/licenses/by/3.0/ Clare Pilgrim @. fobi http://www.obofoundry.org/ontology/fobi CC-BY http://creativecommons.org/licenses/by/3.0/ Pol Castellano Escuder @. @pcastellanoescuder https://github.com/pcastellanoescuder https://github.com/pcastellanoescuder/FoodBiomarkerOntology foodon http://www.obofoundry.org/ontology/foodon CC-BY http://creativecommons.org/licenses/by/3.0/ Damion Dooley @. @Public-Health-Bioinformatics https://github.com/Public-Health-Bioinformatics https://github.com/FoodOntology/foodon fypo http://www.obofoundry.org/ontology/fypo CC-BY http://creativecommons.org/licenses/by/4.0/ Midori Harris @. @mah11 https://github.com/mah11 https://github.com/pombase/fypo genepio http://www.obofoundry.org/ontology/genepio CC-BY http://creativecommons.org/licenses/by/3.0/ Damion Dooley @. https://github.com/GenEpiO/genepio geno http://www.obofoundry.org/ontology/geno CC-BY-SA https://creativecommons.org/licenses/by-sa/2.0/ Matthew Brush @. @mbrush https://github.com/mbrush https://github.com/monarch-initiative/GENO-ontology hsapdv http://www.obofoundry.org/ontology/hsapdv CC-BY http://creativecommons.org/licenses/by/3.0/ bgee @. https://github.com/obophenotype/developmental-stage-ontologies hso http://www.obofoundry.org/ontology/hso CC-BY http://creativecommons.org/licenses/by/3.0/ Fernanda Dorea @. @nandadorea https://github.com/nandadorea https://github.com/SVA-SE/HSO iao http://www.obofoundry.org/ontology/iao CC-BY http://creativecommons.org/licenses/by/4.0/ Jie Zheng @. @zhengj2007 https://github.com/zhengj2007 https://github.com/information-artifact-ontology/IAO iceo http://www.obofoundry.org/ontology/iceo CC-BY http://creativecommons.org/licenses/by/4.0/ Meng LIU @. https://github.com/ontoice/ICEO ico http://www.obofoundry.org/ontology/ico CC-BY http://creativecommons.org/licenses/by/3.0/ Yongqun Oliver He @. @yongqunh https://github.com/yongqunh https://github.com/ICO-ontology/ICO ino http://www.obofoundry.org/ontology/ino CC-BY http://creativecommons.org/licenses/by/3.0/ Yongqun Oliver He @. https://github.com/INO-ontology/ino maxo http://www.obofoundry.org/ontology/maxo CC-BY http://creativecommons.org/licenses/by/3.0/ Leigh Carmody @. @LCCarmody https://github.com/LCCarmody https://github.com/monarch-initiative/MAxO mco http://www.obofoundry.org/ontology/mco CC-BY http://creativecommons.org/licenses/by/3.0/ Citlalli Mejía-Almonte @. https://github.com/microbial-conditions-ontology/microbial-conditions-ontology mf http://www.obofoundry.org/ontology/mf CC-BY http://creativecommons.org/licenses/by/3.0/ Janna Hastings @. @jannahastings https://github.com/jannahastings https://github.com/jannahastings/mental-functioning-ontology mfmo http://www.obofoundry.org/ontology/mfmo CC-BY http://creativecommons.org/licenses/by/3.0/ Robert Druzinsky @. @RDruzinsky https://github.com/RDruzinsky https://github.com/RDruzinsky/feedontology mfoem http://www.obofoundry.org/ontology/mfoem CC-BY http://creativecommons.org/licenses/by/3.0/ Janna Hastings @. @jannahastings https://github.com/jannahastings https://github.com/jannahastings/emotion-ontology mfomd http://www.obofoundry.org/ontology/mfomd CC-BY http://creativecommons.org/licenses/by/3.0/ Janna Hastings @. https://github.com/jannahastings/mental-functioning-ontology mmusdv http://www.obofoundry.org/ontology/mmusdv CC-BY http://creativecommons.org/licenses/by/3.0/ bgee @. https://github.com/obophenotype/developmental-stage-ontologies mpath http://www.obofoundry.org/ontology/mpath CC-BY http://creativecommons.org/licenses/by/3.0/ Paul Schofield @. https://github.com/PaulNSchofield/mpath mpio http://www.obofoundry.org/ontology/mpio CC-BY http://creativecommons.org/licenses/by/4.0/ Mathias Brochhausen @. @mbrochhausen https://github.com/mbrochhausen https://github.com/MPIO-Developers/MPIO mro http://www.obofoundry.org/ontology/mro CC-BY https://creativecommons.org/licenses/by/3.0/ Bjoern Peters @. @bpeters42 https://github.com/bpeters42 https://github.com/IEDB/MRO ms http://www.obofoundry.org/ontology/ms CC-BY https://creativecommons.org/licenses/by/3.0/ Gerhard Mayer @. https://github.com/HUPO-PSI/psi-ms-CV nbo http://www.obofoundry.org/ontology/nbo CC-BY http://creativecommons.org/licenses/by/3.0/ George Gkoutos @. @gkoutos https://github.com/gkoutos https://github.com/obo-behavior/behavior-ontology oae http://www.obofoundry.org/ontology/oae CC-BY http://creativecommons.org/licenses/by/3.0/ Yongqunh He @. https://github.com/OAE-ontology/OAE obcs http://www.obofoundry.org/ontology/obcs CC-BY http://creativecommons.org/licenses/by/3.0/ Jie Zheng @. https://github.com/obcs/obcs obib http://www.obofoundry.org/ontology/obib CC-BY http://creativecommons.org/licenses/by/4.0/ Jie Zheng @. https://github.com/biobanking/biobanking ogg http://www.obofoundry.org/ontology/ogg CC-BY http://creativecommons.org/licenses/by/3.0/ Yongqun Oliver He @. ogms http://www.obofoundry.org/ontology/ogms CC-BY http://creativecommons.org/licenses/by/4.0/ Brian Aevermann @. https://github.com/OGMS/ogms ohd http://www.obofoundry.org/ontology/ohd CC-BY http://creativecommons.org/licenses/by/4.0/ Alan Ruttenberg @. ohmi http://www.obofoundry.org/ontology/ohmi CC-BY http://creativecommons.org/licenses/by/4.0/ Yongqun Oliver He @. https://github.com/ohmi-ontology/ohmi ohpi http://www.obofoundry.org/ontology/ohpi CC-BY http://creativecommons.org/licenses/by/4.0/ Edison Ong @. https://github.com/OHPI/ohpi olatdv http://www.obofoundry.org/ontology/olatdv CC-BY http://creativecommons.org/licenses/by/3.0/ bgee @. https://github.com/obophenotype/developmental-stage-ontologies omp http://www.obofoundry.org/ontology/omp CC-BY http://creativecommons.org/licenses/by/3.0/ James C. Hu @. https://github.com/microbialphenotypes/OMP-ontology one http://www.obofoundry.org/ontology/one CC-BY https://creativecommons.org/licenses/by/4.0/ Chen Yang @. @cyang0128 https://github.com/cyang0128 https://github.com/cyang0128/Nutritional-epidemiologic-ontologies ons http://www.obofoundry.org/ontology/ons CC-BY https://creativecommons.org/licenses/by/4.0/ Francesco Vitali @. @FrancescoVit https://github.com/FrancescoVit https://github.com/enpadasi/Ontology-for-Nutritional-Studies ontoneo http://www.obofoundry.org/ontology/ontoneo CC-BY http://creativecommons.org/licenses/by/3.0/ Fernanda Farinelli @. https://github.com/ontoneo-project/Ontoneo oostt http://www.obofoundry.org/ontology/oostt CC-BY http://creativecommons.org/licenses/by/4.0/ Mathias Brochhausen @. https://github.com/OOSTT/OOSTT opmi http://www.obofoundry.org/ontology/opmi CC-BY http://creativecommons.org/licenses/by/4.0/ Yongqun Oliver He @. https://github.com/OPMI/opmi ornaseq http://www.obofoundry.org/ontology/ornaseq CC-BY http://creativecommons.org/licenses/by/4.0/ Stephen Fisher @. https://github.com/safisher/ornaseq ovae http://www.obofoundry.org/ontology/ovae CC-BY http://creativecommons.org/licenses/by/3.0/ Yongqunh He @. https://github.com/OVAE-Ontology/ovae pato http://www.obofoundry.org/ontology/pato CC-BY http://creativecommons.org/licenses/by/3.0/ George Gkoutos @. @gkoutos https://github.com/gkoutos https://github.com/pato-ontology/pato/ pdumdv http://www.obofoundry.org/ontology/pdumdv CC-BY http://creativecommons.org/licenses/by/3.0/ bgee @. https://github.com/obophenotype/developmental-stage-ontologies phipo http://www.obofoundry.org/ontology/phipo CC-BY http://creativecommons.org/licenses/by/3.0/ Alayne Cuzick @. https://github.com/PHI-base/phipo plana http://www.obofoundry.org/ontology/plana CC-BY http://creativecommons.org/licenses/by/3.0/ Sofia Robb @. https://github.com/obophenotype/planaria-ontology planp http://www.obofoundry.org/ontology/planp CC-BY http://creativecommons.org/licenses/by/3.0/ Sofia Robb @. https://github.com/obophenotype/planarian-phenotype-ontology poro http://www.obofoundry.org/ontology/poro CC-BY http://creativecommons.org/licenses/by/3.0/ Bob Thacker @. https://github.com/obophenotype/porifera-ontology ppo http://www.obofoundry.org/ontology/ppo CC-BY http://creativecommons.org/licenses/by/3.0/ Ramona Walls @. https://github.com/PlantPhenoOntology/PPO pr http://www.obofoundry.org/ontology/pr CC-BY http://creativecommons.org/licenses/by/4.0/ Darren Natale @. @nataled https://github.com/nataled https://github.com/PROconsortium/PRoteinOntology psdo http://www.obofoundry.org/ontology/psdo CC-BY http://creativecommons.org/licenses/by/3.0/ Zach Landis-Lewis @. https://github.com/Display-Lab/psdo pso http://www.obofoundry.org/ontology/pso CC-BY http://creativecommons.org/licenses/by/3.0/ Laurel Cooper @. https://github.com/Planteome/plant-stress-ontology pw http://www.obofoundry.org/ontology/pw CC-BY https://creativecommons.org/licenses/by/4.0/ G. Thomas Hayman @. https://github.com/rat-genome-database/PW-Pathway-Ontology rbo http://www.obofoundry.org/ontology/rbo CC-BY http://creativecommons.org/licenses/by/3.0/ Daniel C. Berrios @. @DanBerrios https://github.com/DanBerrios https://github.com/Radiobiology-Informatics-Consortium/RBO sepio http://www.obofoundry.org/ontology/sepio CC-BY https://creativecommons.org/licenses/by/3.0/ Matthew Brush @. https://github.com/monarch-initiative/SEPIO-ontology stato http://www.obofoundry.org/ontology/stato CC-BY http://creativecommons.org/licenses/by/3.0/ Alejandra Gonzalez-Beltran @. https://github.com/ISA-tools/stato uberon http://www.obofoundry.org/ontology/uberon CC-BY http://creativecommons.org/licenses/by/3.0/ Chris Mungall @. https://github.com/obophenotype/uberon uo http://www.obofoundry.org/ontology/uo CC-BY http://creativecommons.org/licenses/by/3.0/ George Gkoutos @. https://github.com/bio-ontology-research-group/unit-ontology vo http://www.obofoundry.org/ontology/vo CC-BY http://creativecommons.org/licenses/by/3.0/ Yongqunh He @. https://github.com/vaccineontology/VO xao http://www.obofoundry.org/ontology/xao CC-BY http://creativecommons.org/licenses/by/3.0/ Erik Segerdell @. @seger https://github.com/seger https://github.com/xenopus-anatomy/xao xlmod http://www.obofoundry.org/ontology/xlmod CC-BY https://creativecommons.org/licenses/by/3.0/ Gerhard Mayer @. https://github.com/HUPO-PSI/mzIdentML xpo http://www.obofoundry.org/ontology/xpo CC-BY http://creativecommons.org/licenses/by/3.0/ Erik Segerdell @. @seger https://github.com/seger https://github.com/obophenotype/xenopus-phenotype-ontology zeco http://www.obofoundry.org/ontology/zeco CC-BY http://creativecommons.org/licenses/by/3.0/ Yvonne Bradford @. https://github.com/ybradford/zebrafish-experimental-conditions-ontology zfa http://www.obofoundry.org/ontology/zfa CC-BY http://creativecommons.org/licenses/by/3.0/ Ceri Van Slyke @. @cerivs https://github.com/cerivs https://github.com/cerivs/zebrafish-anatomical-ontology zp http://www.obofoundry.org/ontology/zp CC-BY http://creativecommons.org/licenses/by/3.0/ Yvonne Bradford @.*** https://github.com/obophenotype/zebrafish-phenotype-ontology
This table was generated with the following Python code:
from tabulate import tabulate
from bioregistry.external.obofoundry import get_obofoundry from bioregistry.license_standardizer import standardize_license
def main():
rows = [] for key, entry in sorted(get_obofoundry(force_download=True).items()): if entry["deprecated"] or entry["inactive"]: continue license_label = entry.get("license") license_url = entry.get("license.url") if license_label is None and license_url is None: continue # if license_label is None or license_url is None: # raise ValueError if standardize_license(license_url) != standardize_license(license_label): contact_email = entry.get("contact", "") contact_name = entry.get("contact.label", "") contact_github = entry.get("contact.github", "") repository = entry.get("repository", "") rows.append( ( f"[{key}](http://www.obofoundry.org/ontology/{key})", license_label, license_url, contact_name, contact_email, contact_github and f"@{contact_github}", repository, ) ) print( tabulate( rows, headers=[ "prefix", "license_label", "license_url", "contact", "email", "github", "tracker", ], tablefmt="github", ) )if name == "main":
main()— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1638, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACF6DLXYBS64CMONL5Y3JFTUKFMNLANCNFSM5HJJSOJQ . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.
batchelorc
matentzn
cthoyt
As a follow-up to #1635 and with some wisdom from Nico given in related issue #1636, there are several conflicts between the license labels and license URLs. Most of these are due to the lack of specificity of the CC-BY version.
How to fix:
CC-BYtoCC-BY 3.0orCC-BY 4.0See example PR at https://github.com/OBOFoundry/OBOFoundry.github.io/pull/1639, 30 second tutorial video at https://www.youtube.com/watch?v=hGokszEUZtA.
Here's a table of all the ontologies with this issue, plus the actionable contact information on who is responsible for each in case someone is inclined to nudge them:
This table was generated with the following Python code: