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obi-ontology / obi

The Ontology for Biomedical Investigations
http://obi-ontology.org
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OBI vs scicrunch for identifiers for sequencers #1107

Closed cmungall closed 2 months ago

cmungall commented 4 years ago

E.g. both systems have IDs for Illumina HiSeq 2500

I am part of a community (Genomics Standards Consortium) that is trying to decide which system to use. Some of the criteria they care about:

@ramonawalls may have other suggestions

I believe there is a robot template system for sequencers, and changes can be suggested on this tracker, so OBI would seem to fit the community aspect (assuming fast OBI release cycle).

IMO OBI offers a lot of advantages in terms of axioms (isa DNA sequencer, manufactured-by illumina), but these don't really provide advantages to GSC.

OBI has links to PDF spec docs

SCR has links to web pages like https://www.illumina.com/systems/sequencing-platforms/hiseq-2500.html it would seem to be useful to have this in OBI.

Whichever IDs GSC uses, it would seem to be useful for OBI and SCR to coordinate and at least cross-reference one another.

cc @wdduncan

cmungall commented 4 years ago

As an aside one thing that could be useful is additional axiomatization that includes additional metadata about read-length, error rates, etc (this wouldn't be useful for GSC but may serve other use cases)

jamesaoverton commented 4 years ago

While I would like to see devices in OBI (my personal view), and a template would be convenient, I'm worried that OBI developers can't support a huge number of terms with a lot of churn. Do you have a sense of how many terms GSC would need? Or if we could get support?

jamesaoverton commented 4 years ago

Discussed on the OBI call 2020-02-03. There's strong support for doing this. James and Becky will start working on a template, and try to move some existing device terms into it.

turbomam commented 4 years ago

Discussed on 03 February 2020 call. This is an opportunity for OBI to lead/do the job right. We already have good connections with relevant teams, like ENCODE, GSC (MIXS standards), NMDC.

zhengj2007 commented 4 years ago

Here is the device design pattern that OBI current use.

ramonawalls commented 4 years ago

Great to see this happening. Please let me know if you need input from GSC on the lists of machines to include.

jamesaoverton commented 4 years ago

We discussed this on the 2020-02-24 OBI developer call. We're ready to move ahead with #1114, which puts all devices and organizations into ROBOT templates.

@cmungall and @ramonawalls How would GSC submit device terms? If in batches, then we can supply a stripped-down version of the new devices template for them to fill out. If singly, then we will build a GitHub issue template for them to use. In either case, it would be helpful if the submitter(s) have some familiarity with ontologies in general, and ideally with OBI.

ramonawalls commented 4 years ago

I think that @only1chunts and I can work with the GSC group to get a list of terms together and submit them as a batch.

We are still not sure how OBI's terms will relate to the IDs on SciCrunch. Has anyone from OBI reached out to them to coordinate? We hope to avoid duplicate identifiers.

jamesaoverton commented 4 years ago

@beckyjackson and I made the devices sheet and merged it (#1114). Can someone else please take the ball on this?

cmungall commented 2 months ago

I think this can be closed

cmungall commented 2 months ago

I note that OBI has axioms like this:

is_manufactured_byvalueIllumina

This is quite useful for tools that generate submission XML for NCBI!