Assemble list of allowed Organ ontologies

[mshadbolt]

Description

As a metadata team member I want to define a list of organs that are used in `specimen_from_organism.organ.ontology|ontology_label` to ensure consistency in how the terms are applied across projects in the DCP. This ticket stemmed from #1133 **Acceptance Criteria**

• [ ] Summary of use of existing organ and organ part ontologies
• [x] A list of organs and organ ontologies that cover all HCA organs
• [x] Example organ_parts for the more ambiguous 'organs' e.g. blood, bone marrow

[lauraclarke]

@mshadbolt For organ parts, what is your goal?

[ESapenaVentura]

Also, just a clarification: Ontologies that we already have, or that we could potentially have? (e.g. there is no dataset with tissue from the organ part inner lobe of left ear but we could potentially have it in the future because that value is allowed on the ontology we use)

[lauraclarke]

I think having a limited set of organs is a great idea and ensuring we have good examples for organ part but organ part will always be much more detailed so we won't be able to be exhaustive as new bits get defined and different groups discuss what the best terms are

[mshadbolt]

As specified in the ticket I linked to #1133 we decided that we need a tighter set of allowable organs to ensure consistency. These can be specified within our ontology similar to a slim. This is a ticket to define that list and ensure we come up with a list of organs that is likely to cover all data that is currently submitted and will be submitted in the future.

@lauraclarke Some data that is submitted doesn't have what one would classically think of as an organ, e.g. blood & bone marrow, in these cases I want to be clear about what organ should be used as there are multiple ways currently submitted, e.g. hematopoietic system & immune system

[lauraclarke]

This feels like a great list to get feedback on from the metadata-community email list and slack channel. Is this something which might be possible in the new year?

[mshadbolt]

See below for a proposed list of organs.

Open questions/comments/concerns:

Most organs are straight forward but the best way to model some tissue types can be approached from many different angles.

Sometimes I struggled with reconciling the the semantics of organ with the type of tissue a sample is taken from. I pondered whether we should change the name of this field to something like 'source tissue'? e.g. blood, bone marrow.

Bone marrow is one example where we could put it as part of the 'bone' category but I think generally researchers don't generally group marrow with bone since it performs such a different function. Also would it be worth identifying the specific bone the bone marrow was taken from, or is that not something the community would want to know.

Skin is another tricky one in that it is such a large organ that data consumers may want to know both the specific layer of skin a sample was taken from and also the location on the body it was from. One way around this could be to use chained ontology terms but we would need rules in place for how these are used to ensure they are easily interpretable by both humans and computers.

Embryonic/Developmental samples are another tissue type that I wasn't totally sure about but propose having the categories 'embryonic tissue' and 'extraembryonic tissue' to cover all the developing organs as well as things like yolk sac and non-embryonic endoderm.

If we want to strictly enforce these organs how would we enforce validation when a particular organ_part could be a valid child term of multiple organs in the list.

Are @HumanCellAtlas/wranglers aware of any other organs/organ parts that wouldn't fit within these categories?

Does anyone have any other opinions on how we should be grouping organ/organ parts?

ontology_link	organ	organ_part_example
UBERON:0001013	adipose tissue	pericardial fat
UBERON:0000178	blood	umbilical cord blood; venous blood
UBERON:0002371	bone marrow	red bone marrow
UBERON:0002481	bone tissue	proximal epiphysis of tibia
UBERON:0000955	brain	cerebellum; prefrontal cortex
UBERON:0002450	decidua	decidua parietalis
UBERON:0001103	diaphragm	skeletal muscle tissue of diaphragm
UBERON:0005291	embryonic tissue	presumptive gut; blastocyst;endoderm of foregut-midgut junction
UBERON:0001043	esophagus	abdominal part of esophagus
UBERON:0005292	extraembryonic tissue	yolk sac; visceral endoderm
UBERON:0000970	eye	retinal neural layer; corneal epithelium
UBERON:0003889	fallopian tube	ampulla of uterine tube
UBERON:0000948	heart	apex of heart
UBERON:0002113	kidney	cortex of kidney; renal medulla
UBERON:0000059	large intestine	colon; rectum smooth muscle tissue
UBERON:0002107	liver	caudate lobe of liver
UBERON:0002048	lung	lower lobe of left lung
UBERON:0000029	lymph node	mediastinal lymph node
UBERON:0001911	mammary gland	lobule of mammary gland
UBERON:0000165	mouth	sublingual gland
UBERON:0000004	nose	midnasal cavity
UBERON:0000992	ovary	corpus luteum
UBERON:0001264	pancreas	islet of Langerhans; pancreas head parenchyma
UBERON:0001987	placenta	decidua basalis (?)
UBERON:0002367	prostate gland	posterior lobe of prostate
UBERON:0014892	skeletal muscle organ	biceps brachii
UBERON:0002097	skin of body	lower back skin||reticular layer of dermis
UBERON:0002108	small intestine	ileum; jejunum
UBERON:0002240	spinal cord	lumbar spinal cord white matter
UBERON:0002106	spleen	hilum of spleen
UBERON:0000945	stomach	serosa of fundus of stomach
UBERON:0000473	testis	Leydig cell region of testis
UBERON:0002370	thymus	cortex of thymus
UBERON:0001723	tongue	horny papilla of tongue
UBERON:0003126	trachea	trachealis
UBERON:0000056	ureter	ureter smooth muscle
UBERON:0000057	urethra	urethra urothelium
UBERON:0001255	urinary bladder	urinary bladder detrusor smooth muscle
UBERON:0000995	uterus

also pinging @zoependlington so she is aware of the conversation

[tburdett]

This looks great @mshadbolt, nice work. On the question of validation - there's a really good discussion to have here about how much of this should be structured into the ontology (UBERON or our own application ontology) and whether there's axiomatisation that can help us, and that we can use in validation. Pinging @simonjupp as well as Zoe for thoughts on that

[zperova]

thank you @mshadbolt As we discussed I think anything related to development will be a special case as some "organs" do not exist and some exist only at a certain age and become something else afterwards, and we can also consider the use of "anatomical system".

[lauraclarke]

This feels like a great discussion topic with the metadata community. I think we need to decide what our desired outcome is though before we pose the question otherwise we might just end up with a lot of discussions without any concrete outcome.

I see the consistency goal and I appreciate it looks better for there to be consistency in particular in the organ selection as it helps give much better facets from a search perspective but is there value from any other angles than the discovery one? What about the organ part? Are we striving for consistency or are we wanting to ensure that the anatomy definitions are sufficiently good and of the right granularity that people aren't put in a position of making sub-optimal annotations because there isn't anything better?

[lauraclarke]

This seems like a good list to compare our allowable organ rather than organ part terms. Is there a good middle ground between this and each discrete organ for that top-level list?

[mshadbolt]

I am not quite sure I understand, are you suggesting we use systems rather than organs? How would we reconcile when a single organ or tissue type can be a part of multiple systems? Or are you suggesting we also have a system level metadata field?

[lauraclarke]

I thought one goal here was to introduce consistency for limiting the number of terms that were acceptable in the organ field so we don't get say colon and large intestine.

I figured this set of 14 systems was a good starting point to establishing the list, but recognise that some of them are so high level it might be better to allow the discrete organs where there are ones, so rather than only allowing endocrine system to be specified, having pancreas, thymus, adrenal glands and whatever other endocrine organs existed.

It would be good to see if these system names could be derived from the ontology though as that would link up nicely, so all organs could be linked to one or more of these systems

[mshadbolt]

I feel quite strongly that if this field is labelled as 'organ' that it shouldn't contain the name of a system. But would be good to get feedback from others and the community about what they would expect from this field.

Yes there is a way of getting an associated system from an organ term in the ontology but it is possible for one term to be a part of multiple systems, e.g. blood is a part of immune system and haematopoietic system

[pnejad]

I agree @mshadbolt. I believe there was a discussion with the UX team in this repo or the wrangling repo (It could have also been at one of our F2F meetings) on why we should not use system. I'll look around in my notes.

[pnejad]

I like @zperova's idea of using "anatomical system" for special cases where 'organ' does not exist.

[jahilton]

Would it make sense to split into separate 'organs' & 'systems' fields?

[lauraclarke]

I would suggest if we have a system field that we make sure it can be automatically filled out rather than expecting submitters to provide an additional piece of information.

The list I posted above was to provide a helpful starting point to consider what the reduced list of organs should be rather than necessarily to be the terms which went in the organ field.

Endeavouring to be consistent with the organ system categorisation that the executive uses seems like a good idea

[zperova]

I think systems field will be very helpful for display of the data in the Browser, but should be automatically assigned based on the organ (so the organs will be grouped based on some algorithm by the Browser in the absence of ontology expansion). We could add a systems field in the metadata and fill in all the relevant systems however that is not a sustainable solution.