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Improve annotation of cross-references #103

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cthoyt opened this issue Jun 29, 2023 · 5 comments
Open

Improve annotation of cross-references #103

cthoyt opened this issue Jun 29, 2023 · 5 comments

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@cthoyt
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cthoyt commented Jun 29, 2023

I found that CLO makes cross-references using the rdfs:seeAlso predicate instead of something a bit more fit-for-purpose like oboInOwl:hasDbXref or skos:exactMatch.

I also found that these rdfs:seeAlso annotations point to strings that potentially contain multiple CURIEs, with varying degrees of heterogeneity in how they're written.

Can you give a bit of insight into why the cross-references were encoded this way?

I wrote a script that attempts to parse and standardize them using the Bioregistry. I posted the output in an SSSOM file in this gist. Would you be interested for me to contribute these back in a more standardized way to CLO?
@cthoyt cthoyt mentioned this issue Jun 29, 2023
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@cthoyt
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cthoyt commented Jun 29, 2023

CC @yongqunh

cthoyt added a commit to biopragmatics/biomappings that referenced this issue Jul 3, 2023
@cthoyt
Add CLO processing notebook (#133)
dc39c45 
The [Cell Line Ontology (CLO)](https://bioregistry.io/registry/clo) is a
detailed resource, however it does not follow standard OBO modeling
pattern for cross-references that either a predicate from
[SKOS](https://bioregistry.io/skos) or `oboInOwl:hasDbXref` to point to
a single CURIE encoded as a string. Instead, it uses `rdfs:seeAlso` with
a combination of non-standard CURIEs that are either comma or semi-colon
delimited.

Depends on:
- biopragmatics/bioregistry#896
- CLO-ontology/CLO#103
@yongqunh
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@cthoyt That's great! We would like to get your contribution.

Sorry for the delayed reply since I just came back from a two-week travel. We have recently had Dr. Jie Zheng join our group. I would suggest having her involved as well. Do you have a time for a meeting on this?
Thanks.

@cthoyt
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cthoyt commented Jul 17, 2023 •
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Hi @yongqunh and @zhengj2007, I am also just back from vacation and at a project meeting this week. Next week I am relatively free and on east coast time. It would be great to plan a video conference. For me, around 11AM is best, but I'm flexible. My email is [email protected] if you would rather coordinate on that channel, too (or on slack)

@zhengj2007
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I am available around 11:00 EST Monday, Tuesday, and Thursday next week. It would be great to discuss it with you. @cthoyt

@zhengj2007
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See related discussion on what annotation property should be used to indicate the mapped/equivalent terms

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@yongqunh @cthoyt @zhengj2007