New term requests to support Daphnia magna anatomical annotations

[proccaserra]

This is a batch request for term addition, hence the table

Daphnia magnaAnatomical ID	System/structure (Display Name)	Parent Structure	definition	definition source	parent term	synonym	editor	orcid	Suggested Parent Class in UBERON	UBERON identifier	UBERON class label	SKOS relation to UBERON class	Comment
2200	Food Groove	Digestive	elongated median channel between bases of thoracic limbs, where the food is transferred to the mouthpart	DOI: https://doi.org/10.1098/rstb.1991.0001	digestive system	food channel	Mee Siing Ngu	0000-0002-7638-4659	?	?	?	?	TERM REQUEST
2510	Labral Gland Cell	Labrum	cell at the base and in the median part of labrum	PMID: 29929348	labrum		Mee Siing Ngu	0000-0002-7638-4659	?	?	?	?	TERM REQUEST
4110	Protopodite	Antenna	basal part of each antenna; relatively long, bearing two- to four-segmented dorsal and ventral branches (rami)	PMID: 24540161	antenna	protopod	Mee Siing Ngu	0000-0002-7638-4659	?				TERM REQUEST
4120	Ramus	Antenna	dorsal or ventral branches of antennae	PMID: 24540161	protopodite		Mee Siing Ngu	0000-0002-7638-4659	?				TERM REQUEST
4130	Seta	Ramus	one of numerous bristle-like projections extending from appendage or body	PMID: 24540161	ramus		Mee Siing Ngu	0000-0002-7638-4659	UBERON	http://purl.obolibrary.org/obo/UBERON_0013703	integumentary projection	broader	TERM REQUEST
4210	Copulatory Hook (Male)	Thoracic Limb 1	chitinized hooks of male Daphnia that are used for clasping the females during copulation	ISBN:9057821516 9789057821516 or https://doi.org/10.1093/plankt/fbl041	thoracic limb 1	clasping hook	Mee Siing Ngu	0000-0002-7638-4659	?				TERM REQUEST
4220	Seta	Thoracic Limb 1	bristle-like projection extending from thoracic limb 1	ISBN:9057821516 9789057821516 or https://doi.org/10.1093/plankt/fbl041	thoracic limb 1		Mee Siing Ngu	0000-0002-7638-4659	UBERON	http://purl.obolibrary.org/obo/UBERON_0013703	integumentary projection	broader	TERM REQUEST
4410	Filter Plate 3	Thoracic Limb 3	food filtering apparatus on the gnathobases of thoracic limbs 3	https://doi.org/10.1098/rstb.1991.0001	thoracic limb 3	filter	Mee Siing Ngu	0000-0002-7638-4659	?				TERM REQUEST
4510	Filter Plate 4	Thoracic Limb 4	food filtering apparatus on the gnathobases of thoracic limbs 4	https://doi.org/10.1098/rstb.1991.0001	thoracic limb 4	filter	Mee Siing Ngu	0000-0002-7638-4659	?				TERM REQUEST
5020	Antennule Muscle (Male)	Muscular	muscle in the antennule	https://doi.org/10.1002/iroh.19310260104	musculoskeletal		Mee Siing Ngu	0000-0002-7638-4659	UBERON	http://purl.obolibrary.org/obo/UBERON_0001630	muscle organ	broader	TERM REQUEST
5030	Anterior Carapace Adductor Muscle	Muscular	muscle attached to the carapace that pulls it to the body	https://doi.org/10.1098/rstb.1991.0001	musculoskeletal		Mee Siing Ngu	0000-0002-7638-4659	UBERON	http://purl.obolibrary.org/obo/UBERON_0001630	muscle organ	broader	TERM REQUEST
5040	Anterior Rotator Muscle of Mandible	Muscular	anterior rotator muscle of the mandible	https://doi.org/10.1002/iroh.19310260104	musculoskeletal		Mee Siing Ngu	0000-0002-7638-4659	UBERON	http://purl.obolibrary.org/obo/UBERON_0001630	muscle organ	broader	TERM REQUEST
5050	Circular Muscle	Muscular	muscle encasing the cecum and gut	https://doi.org/10.1016/C2011-0-05143-8	musculoskeletal		Mee Siing Ngu	0000-0002-7638-4659	UBERON	http://purl.obolibrary.org/obo/UBERON_2005279	enteric circular muscle	narrower	TERM REQUEST
5060	Dorsal Longitudinal Muscle	Muscular	dorsal muscle that extends along each side of the body	https://doi.org/10.1098/rstb.1991.0001	musculoskeletal		Mee Siing Ngu	0000-0002-7638-4659	UBERON	http://purl.obolibrary.org/obo/UBERON_0001630	muscle organ	broader	TERM REQUEST
5070	Esophageal Dilator Muscle	Muscular	dilator muscle of the esophagus	https://doi.org/10.1098/rstb.1991.0001	musculoskeletal		Mee Siing Ngu	0000-0002-7638-4659	UBERON	http://purl.obolibrary.org/obo/UBERON_0003832	easophagus muscle	broader	TERM REQUEST
5080	Horizontal Muscle	Muscular	horizontal muscle along each side of the body	https://doi.org/10.1098/rstb.1991.0001	musculoskeletal		Mee Siing Ngu	0000-0002-7638-4659	UBERON	http://purl.obolibrary.org/obo/UBERON_0001630	muscle organ	broader	TERM REQUEST
5090	Oblique-Lateral Muscle	Muscular	muscle branching from the ventral longitudinal muscle	https://doi.org/10.1002/iroh.19310260104	musculoskeletal		Mee Siing Ngu	0000-0002-7638-4659	UBERON	http://purl.obolibrary.org/obo/UBERON_0001630	muscle organ	broader	TERM REQUEST
5100	Postabdominal Muscle	Muscular	adductor muscle on the abdomen/postabdomen	https://doi.org/10.1002/iroh.19310260104	musculoskeletal		Mee Siing Ngu	0000-0002-7638-4659	UBERON	http://purl.obolibrary.org/obo/UBERON_0001630	muscle organ	broader	TERM REQUEST
5110	Posterior Carapace Adductor Muscle	Muscular	muscle attached to the carapace that pulls it to the body	https://doi.org/10.1098/rstb.1991.0001	musculoskeletal		Mee Siing Ngu	0000-0002-7638-4659	UBERON	http://purl.obolibrary.org/obo/UBERON_0001630	muscle organ	broader	TERM REQUEST
5120	Posterior Rotator Muscle of Mandible	Muscular	posterior rotator muscle of the mandible	https://doi.org/10.1002/iroh.19310260104	musculoskeletal		Mee Siing Ngu	0000-0002-7638-4659	UBERON	http://purl.obolibrary.org/obo/UBERON_0001630	muscle organ	broader	TERM REQUEST
5130	Rectal Dilator Muscle	Muscular	dilator muscle around the rectum	https://doi.org/10.1098/rstb.1991.0001	musculoskeletal		Mee Siing Ngu	0000-0002-7638-4659	UBERON	http://purl.obolibrary.org/obo/UBERON_0018112	rectum smooth muscle tissue	narrower	TERM REQUEST
7000	Postabdomen		recurved posteriormost region of trunk	https://www.ncbi.nlm.nih.gov/books/NBK2036	abdomen		Mee Siing Ngu	0000-0002-7638-4659	?	?	?	?	TERM REQUEST
7100	Abdominal Process	Postabdomen	dorsal processes projecting from border of trunk and postabdomen; one is considered to serve in closing off brood chamber posteriorly	https://www.ncbi.nlm.nih.gov/books/NBK2036	postabdomen		Mee Siing Ngu	0000-0002-7638-4659	UBERON	http://purl.obolibrary.org/obo/UBERON_0013703	integumentary projection	broader	TERM REQUEST
7300	Postabdominal Claw	Postabdomen	one of two relatively short, claw-shaped projections at end of postabomen	https://www.ncbi.nlm.nih.gov/books/NBK2036	postabdomen		Mee Siing Ngu	0000-0002-7638-4659	UBERON	http://purl.obolibrary.org/obo/UBERON_0013703	integumentary projection	broader	TERM REQUEST
8420	Gonopore (Male)	Testis	ejaculatory opening on the postabdomen of the male daphnia	ISBN:9057821516 9789057821516 or https://doi.org/10.1093/plankt/fbl041	sperm duct	ejaculatory opening	Mee Siing Ngu	0000-0002-7638-4659	UBERON	http://purl.obolibrary.org/obo/UBERON_0001349	externally connecting tube lumen	broader	TERM REQUEST

Daphnia magnaAnatomical ID System/structure (Display Name) Parent Structure definition definition source parent term synonym editor orcid Suggested Parent Class in UBERON UBERON identifier UBERON class label SKOS relation to UBERON class Comment 2200 Food Groove Digestive elongated median channel between bases of thoracic limbs, where the food is transferred to the mouthpart DOI: https://doi.org/10.1098/rstb.1991.0001 digestive system food channel Mee Siing Ngu 0000-0002-7638-4659 ? ? ? ? TERM REQUEST 2510 Labral Gland Cell Labrum cell at the base and in the median part of labrum PMID: 29929348 labrum Mee Siing Ngu 0000-0002-7638-4659 ? ? ? ? TERM REQUEST 4110 Protopodite Antenna basal part of each antenna; relatively long, bearing two- to four-segmented dorsal and ventral branches (rami) PMID: 24540161 antenna protopod Mee Siing Ngu 0000-0002-7638-4659 ? TERM REQUEST 4120 Ramus Antenna dorsal or ventral branches of antennae PMID: 24540161 protopodite Mee Siing Ngu 0000-0002-7638-4659 ? TERM REQUEST 4130 Seta Ramus one of numerous bristle-like projections extending from appendage or body PMID: 24540161 ramus Mee Siing Ngu 0000-0002-7638-4659 UBERON http://purl.obolibrary.org/obo/UBERON_0013703 integumentary projection broader TERM REQUEST 4210 Copulatory Hook (Male) Thoracic Limb 1 chitinized hooks of male Daphnia that are used for clasping the females during copulation ISBN:9057821516 9789057821516 or https://doi.org/10.1093/plankt/fbl041 thoracic limb 1 clasping hook Mee Siing Ngu 0000-0002-7638-4659 ? TERM REQUEST 4220 Seta Thoracic Limb 1 bristle-like projection extending from thoracic limb 1 ISBN:9057821516 9789057821516 or https://doi.org/10.1093/plankt/fbl041 thoracic limb 1 Mee Siing Ngu 0000-0002-7638-4659 UBERON http://purl.obolibrary.org/obo/UBERON_0013703 integumentary projection broader TERM REQUEST 4410 Filter Plate 3 Thoracic Limb 3 food filtering apparatus on the gnathobases of thoracic limbs 3 https://doi.org/10.1098/rstb.1991.0001 thoracic limb 3 filter Mee Siing Ngu 0000-0002-7638-4659 ? TERM REQUEST 4510 Filter Plate 4 Thoracic Limb 4 food filtering apparatus on the gnathobases of thoracic limbs 4 https://doi.org/10.1098/rstb.1991.0001 thoracic limb 4 filter Mee Siing Ngu 0000-0002-7638-4659 ? TERM REQUEST 5020 Antennule Muscle (Male) Muscular muscle in the antennule https://doi.org/10.1002/iroh.19310260104 musculoskeletal Mee Siing Ngu 0000-0002-7638-4659 UBERON http://purl.obolibrary.org/obo/UBERON_0001630 muscle organ broader TERM REQUEST 5030 Anterior Carapace Adductor Muscle Muscular muscle attached to the carapace that pulls it to the body https://doi.org/10.1098/rstb.1991.0001 musculoskeletal Mee Siing Ngu 0000-0002-7638-4659 UBERON http://purl.obolibrary.org/obo/UBERON_0001630 muscle organ broader TERM REQUEST 5040 Anterior Rotator Muscle of Mandible Muscular anterior rotator muscle of the mandible https://doi.org/10.1002/iroh.19310260104 musculoskeletal Mee Siing Ngu 0000-0002-7638-4659 UBERON http://purl.obolibrary.org/obo/UBERON_0001630 muscle organ broader TERM REQUEST 5050 Circular Muscle Muscular muscle encasing the cecum and gut https://doi.org/10.1016/C2011-0-05143-8 musculoskeletal Mee Siing Ngu 0000-0002-7638-4659 UBERON http://purl.obolibrary.org/obo/UBERON_2005279 enteric circular muscle narrower TERM REQUEST 5060 Dorsal Longitudinal Muscle Muscular dorsal muscle that extends along each side of the body https://doi.org/10.1098/rstb.1991.0001 musculoskeletal Mee Siing Ngu 0000-0002-7638-4659 UBERON http://purl.obolibrary.org/obo/UBERON_0001630 muscle organ broader TERM REQUEST 5070 Esophageal Dilator Muscle Muscular dilator muscle of the esophagus https://doi.org/10.1098/rstb.1991.0001 musculoskeletal Mee Siing Ngu 0000-0002-7638-4659 UBERON http://purl.obolibrary.org/obo/UBERON_0003832 easophagus muscle broader TERM REQUEST 5080 Horizontal Muscle Muscular horizontal muscle along each side of the body https://doi.org/10.1098/rstb.1991.0001 musculoskeletal Mee Siing Ngu 0000-0002-7638-4659 UBERON http://purl.obolibrary.org/obo/UBERON_0001630 muscle organ broader TERM REQUEST 5090 Oblique-Lateral Muscle Muscular muscle branching from the ventral longitudinal muscle https://doi.org/10.1002/iroh.19310260104 musculoskeletal Mee Siing Ngu 0000-0002-7638-4659 UBERON http://purl.obolibrary.org/obo/UBERON_0001630 muscle organ broader TERM REQUEST 5100 Postabdominal Muscle Muscular adductor muscle on the abdomen/postabdomen https://doi.org/10.1002/iroh.19310260104 musculoskeletal Mee Siing Ngu 0000-0002-7638-4659 UBERON http://purl.obolibrary.org/obo/UBERON_0001630 muscle organ broader TERM REQUEST 5110 Posterior Carapace Adductor Muscle Muscular muscle attached to the carapace that pulls it to the body https://doi.org/10.1098/rstb.1991.0001 musculoskeletal Mee Siing Ngu 0000-0002-7638-4659 UBERON http://purl.obolibrary.org/obo/UBERON_0001630 muscle organ broader TERM REQUEST 5120 Posterior Rotator Muscle of Mandible Muscular posterior rotator muscle of the mandible https://doi.org/10.1002/iroh.19310260104 musculoskeletal Mee Siing Ngu 0000-0002-7638-4659 UBERON http://purl.obolibrary.org/obo/UBERON_0001630 muscle organ broader TERM REQUEST 5130 Rectal Dilator Muscle Muscular dilator muscle around the rectum https://doi.org/10.1098/rstb.1991.0001 musculoskeletal Mee Siing Ngu 0000-0002-7638-4659 UBERON http://purl.obolibrary.org/obo/UBERON_0018112 rectum smooth muscle tissue narrower TERM REQUEST 7000 Postabdomen recurved posteriormost region of trunk https://www.ncbi.nlm.nih.gov/books/NBK2036 abdomen Mee Siing Ngu 0000-0002-7638-4659 ? ? ? ? TERM REQUEST 7100 Abdominal Process Postabdomen dorsal processes projecting from border of trunk and postabdomen; one is considered to serve in closing off brood chamber posteriorly https://www.ncbi.nlm.nih.gov/books/NBK2036 postabdomen Mee Siing Ngu 0000-0002-7638-4659 UBERON http://purl.obolibrary.org/obo/UBERON_0013703 integumentary projection broader TERM REQUEST 7300 Postabdominal Claw Postabdomen one of two relatively short, claw-shaped projections at end of postabomen https://www.ncbi.nlm.nih.gov/books/NBK2036 postabdomen Mee Siing Ngu 0000-0002-7638-4659 UBERON http://purl.obolibrary.org/obo/UBERON_0013703 integumentary projection broader TERM REQUEST 8420 Gonopore (Male) Testis ejaculatory opening on the postabdomen of the male daphnia ISBN:9057821516 9789057821516 or https://doi.org/10.1093/plankt/fbl041 sperm duct ejaculatory opening Mee Siing Ngu 0000-0002-7638-4659 UBERON http://purl.obolibrary.org/obo/UBERON_0001349 externally connecting tube lumen broader TERM REQUEST

[shawntanzk]

@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!

[proccaserra]

@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!

[ghost]

@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.

uberon_template.xlsx

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.

[MeeSiing]

@proccaserra @bvarner-ebi thank you for your help and information. I will use the template as a guide.

[shawntanzk]

@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 :)

[proccaserra]

@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

[ghost]

@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.

[MeeSiing]

@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.

[shawntanzk]

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

[proccaserra]

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.

[cmungall]

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:

• what's the relationship of the proposed "labrum" term to the existing uberon insect labrum. Should the existing uberon term be generalized?
• similarly how best to generalize the current "insect thorax" to all arthropods
• how to deal with serial homology

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:

• antenna
• testis
• muscle

I would try and reuse patterns as much as possible but we don't have great docs for this

[proccaserra]

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

[ghost]

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.

[proccaserra]

Hi @bvarner-ebi , thank for checking. it sounds about right. If we need terms from uberon, we'll open an issue.