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The Ontology for Biomedical Investigations
http://obi-ontology.org
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Consider coordinating with Wikipedia #1001

Open jamesaoverton opened 5 years ago

jamesaoverton commented 5 years ago

Looking at #1000 on the 2019-03-04 call, the first thing we did was look at the provided Wikipedia link. Bjoern raised the point that we could try to coordinate more closely with Wikipedia (and/or Wikidata). Over the years since OBI began, Wikipedia entries have drastically improved.

Wikipedia entries include a lot of information that OBI does not, but the first paragraph almost always includes a definition (or something like a definition) that we could coordinate with.

We have a lot of Wikipedia links in OBI. To support some degree of automation, we could add a column to our templates that points to a Wikipedia page. Then we could automatically check for recent changes to Wikipedia pages.

We could also check for matching labels, in general, or for outstanding term requests. The latter could help add more terms to OBI faster.

rvita commented 5 years ago

I asked Andrew Su at wikidata about adding OBI terms to wikipedia & wikidata (b/c he helps IEDB get terms in wikidata). For wikipedia- he suggests we post at https://en.wikipedia.org/wiki/WT:MCB to explore both the "how do people feel" issue and technical paths to get there. For wikidata- he says "We are very interested in adding OBI mappings to wikidata, but that of course would be dependent on a compatible license. The license for OBI is CC-BY 3.0 and as a general rule, CC-BY is not compatible with CC0 because of the attribution requirement. And everything in Wikidata must be CC0. But, I'm not sure if the mere fact that https://www.wikidata.org/wiki/Q332126 is the same thing as OBI_0000661 is subject to the OBI data license. (That's in contrast to the definition and the class hierarchy of OBI, which clearly is subject to the data license.) If the mapping is outside the scope of the data license, then you/we could upload the mappings to wikidata with no change in the OBI CC-BY license. Of course, OBI could also make this explicit by releasing a mapping file under CC0." He would be happy to be further engaged by OBI on this topic. I hope this is helpful? -Randi

cstoeckert commented 5 years ago

Randi, This is very helpful and something to discuss on an upcoming call. Thanks! Chris

From: rvita notifications@github.com Reply-To: obi-ontology/obi reply@reply.github.com Date: Tuesday, March 5, 2019 at 6:59 PM To: obi-ontology/obi obi@noreply.github.com Cc: Subscribed subscribed@noreply.github.com Subject: [External] Re: [obi-ontology/obi] Consider coordinating with Wikipedia (#1001)

I asked Andrew Su at wikidata about adding OBI terms to wikipedia & wikidata (b/c he helps IEDB get terms in wikidata). For wikipedia- he suggests we post at https://en.wikipedia.org/wiki/WT:MCB to explore both the "how do people feel" issue and technical paths to get there. For wikidata- he says "We are very interested in adding OBI mappings to wikidata, but that of course would be dependent on a compatible license. The license for OBI is CC-BY 3.0 and as a general rule, CC-BY is not compatible with CC0 because of the attribution requirement. And everything in Wikidata must be CC0. But, I'm not sure if the mere fact that https://www.wikidata.org/wiki/Q332126 is the same thing as OBI_0000661 is subject to the OBI data license. (That's in contrast to the definition and the class hierarchy of OBI, which clearly is subject to the data license.) If the mapping is outside the scope of the data license, then you/we could upload the mappings to wikidata with no change in the OBI CC-BY license. Of course, OBI could also make this explicit by releasing a mapping file under CC0." He would be happy to be further engaged by OBI on this topic. I hope this is helpful? -Randi

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turbomam commented 5 years ago

Thanks Randi.

Chris, didn't you encourage me to use CC0 for TURBO? I thought that was the OBO preference, although CC-BY is tolerated?

http://www.obofoundry.org/principles/fp-001-open.html

jamesaoverton commented 5 years ago

@turbomam Historically OBO has advocated CC-BY licenses, which require attribution in ways that tend to support academic norms for citation. In recent years there has been increasing support for CC0 instead, to encourage better interoperability and reuse.

It's complicated, and there are good reasons in support of both CC-BY and CC0. See Principle 1: Open, and discussion: http://www.obofoundry.org/principles/fp-001-open.html

cmungall commented 5 years ago

For MONDO we make a subset available that is CC-0 which includes logical axioms and excludes things like textual definitions (which are often sourced from multiple places).

rvita commented 5 years ago

@andrewsu said that if OBI sets just the term names and respective OBI ids as CC-0, we will be compatible with wikidata. Andrew is available for the Apr 29 or May 13 regular OBI call, but notes that @cmungall should also be able to tell OBI how accomplish this selective use of a license.