Closed proccaserra closed 2 years ago
@bvarner-ebi - can I leave this with you? I would recommend using templates for such a huge add. @proccaserra - I think there are some issues with your MD formatting that is causing misalignment - please do check. It would also be good if you could work with @bvarner-ebi (if he takes this ticket) to create more ontology-conforming definitions for the terms requested. @bvarner-ebi - I will assign this to you for now, but do let me know if you need help etc. Thanks!
@shawntanzk thank you for picking this up so quickly. @bvarner-ebi , I have updated the issue to clear the error in the markdown table. I can also provide a tsv file matching the template that would suit the process if you point me to it.
much appreciated!
@proccaserra, thank you for the potential Uberon contributions.
To suggest new terms, we ask you provide information as requested in the new term request template: https://github.com/obophenotype/uberon/issues/new?assignees=&labels=new+term+request&template=a_adding_term.md This will help an editor better understand your request. You can use the attached template as a guide.
As noted above, the definitions should be reviewed and written to align with Uberon standards. My recommendation is to review similar terms in Uberon and pattern your definitions off of those.
Please note there is currently a backlog of new term requests, so it may be a few months before this ticket would be started once the requested information is provided.
@proccaserra @bvarner-ebi thank you for your help and information. I will use the template as a guide.
@proccaserra btws this might help with definitions: https://douroucouli.wordpress.com/2019/07/08/ontotip-write-simple-concise-clear-operational-textual-definitions/
I would advice you write it in genus-differentia method stated in the above :)
@shawntanzk indeed, this is best practice. I was brokering the submission on behalf of @MeeSiing. @MeeSiing happy to assist if you further questions.
@bvarner-ebi , @shawntanzk regarding the timeline for processing the terms and to avoid any delay, were there any 'red-flags' from this list of terms?
By red-flag
, I mean any constraint on Uberon which would lead to rejecting a term. For instance, a term such as 'post abdomen' defined as 'recurved posteriormost region of trunk' (which once rephrased would be: a part of the trunk located in the most posterior region and which is recurved' ?).
thx
@MeeSiing, @proccaserra, I noticed you have included a field called "Daphnia magnaAnatomical ID". Are these coming from an atlas or do you by chance already have a Daphnia magna-focused ontology?
Context of this question: Uberon covers metazoa, but has a vertebrate bias. Most, if not all, of these terms would require taxon restrictions. For example, food grooves and filter plates are not present in all metazoa, and would need to be annotated as such in Uberon.
@proccaserra Thank you for the question about 'red-flags'. Please also point out to me if you have seen some and I will work on them. truly appreciate your help. @bvarner-ebi these terms are daphnia specific and are from the daphnia histology atlas that I am developing http://daphnia.io. The ontology list can be found here (http://daphnia.io/assets/downloads/DaHRA/S2_File_Anatomy_ontology.xlsx). I compiled them from different resources and selected this list based on their relevance to current studies.
Thanks @MeeSiing - just so we understand, what's your use case of adding the terms to uberon? I ask as I wonder if it makes more sense to convert the xls file into a species-specific ontology and link it to uberon using a bridge or SSSOM - we can probably provide some support for you with that too.
Would also like some input on this from @cmungall
The context is the following: The project we are involved in currently working with 6 species [Homo sapiens (cells), Xenopus laevis, Danio rerio, Drosophila melanogaster, C. elegans, Daphnia magna] exploring the effect of chemical agents (250 of them) with omics and imaging based phenotyping. Since nothing (to my knowledge) exists for Daphnia and there is a need to go cross-species, the idea of pushing term to Uberon appealed as it could/would save having to maintain another resource. Having said that, it seems an anatomy ontology for Daphnia magna would be straightforward to produce (technically speaking). Yet, if we can spare a mapping. Thank you all.
Hi @proccaserra
Short story: a separate ontology is probably the best bet in the short term
I'm open to incorporating directly in uberon but if we do this, we need to do it right, and this will require expertise in both comparative arthropod anatomy and familiarity with uberon patterns (there used to be an active arthropod anatomy ontology community, but I am not sure how active they are). I can help a bit here but it will be a bit of work
These are the kinds of things we'd need to address:
If you start with your own ontology then you can go ahead and make terms like "thoracic limb 4" without getting bogged down in homology questions.
If you do make your own ontology you can reuse some uberon classes that should be safe for pan-arthropod usage:
I would try and reuse patterns as much as possible but we don't have great docs for this
Hi @cmungall
Thank you for the insights. I was indeed concerned about these homologous structures. We can work with @MeeSiing to generate the species specific ontology and then work with @shawntanzk and @matentzn to develop an SSSOM file against UBERON.
We might even help with the doc in the process. thx
Hi, @proccaserra, checking in if this ticket can be closed. Based on your comment above, it seems you plan to work on generating a species-specific ontology instead of adding these terms directly into Uberon.
Hi @bvarner-ebi , thank for checking. it sounds about right. If we need terms from uberon, we'll open an issue.
This is a batch request for term addition, hence the table