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The Ontology for Biomedical Investigations
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Names of sequencing software #1175

Open ddooley opened 4 years ago

ddooley commented 4 years ago

Does OBI want to take on lists of sequencing assembly software? If so, I can create NTRS for Unicycler, Shovil, Velvet, Canu, Spades. Its possible a "software template" could be fashioned for these.

jamesaoverton commented 4 years ago

Hi @ddooley. I'd kinda like to have everything like this in OBI, along with devices. A new template would make sense.

My concern is that SWO and EDAM have a bunch of software terms already. They aren't in OBO, but we don't want to duplicate effort either. I'm not sure what's best.

ddooley commented 4 years ago

We will make a robot template, and will bring in a few existing items, covering the software application class/domain. Base on device template.

cmungall commented 3 years ago

We have a ticket about SWO/EDAM here: https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1040

If licensing issues can be resolved then I suggest using one of these two ontologies rather than duplicating effort. Perhaps we could work with these communities to implement a template approach.

Alternatively, if licensing issues cannot be resolved I suggest instead going via Wikidata.

btw, I am not sure if this is intentional, but OBI sometimes uses instances for software: http://www.ontobee.org/ontology/OBI?iri=http://purl.obolibrary.org/obo/OBI_0000713

image

ddooley commented 3 years ago

Personally I think an instance of some software at best might be a version of it, or more likely, a version that has on my desktop just been infected by a virus! But I leave it to others to determine the OBI position on that.

allysonlister commented 3 years ago

Good afternoon all!

I'm part of the team that maintains SWO, and many years ago I was one of the developers of OBI too. I was wondering if it might be worth me joining an OBI call at some point to talk about points where our two ontologies converge and perhaps could have a more organized approach to using each others' terms?

Thanks :)

bpeters42 commented 3 years ago

I think that would be excellent Allyson! We have our regular call today (still the same slot from when you were a member:) We should put this on the agenda. I know we talked about coordinating before, and I simply forgot where we left off.

On Mon, Jun 21, 2021 at 6:17 AM Allyson Lister @.***> wrote:

Good afternoon all!

I'm part of the team that maintains SWO, and many years ago I was one of the developers of OBI too. I was wondering if it might be worth me joining an OBI call at some point to talk about points where our two ontologies converge and perhaps could have a more organized approach to using each others' terms?

Thanks :)

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-- Bjoern Peters Professor La Jolla Institute for Immunology 9420 Athena Circle La Jolla, CA 92037, USA Tel: 858/752-6914 Fax: 858/752-6987 http://www.liai.org/pages/faculty-peters

allysonlister commented 3 years ago

Thanks Bjoern! Lovely to hear from you 🙂 I'm happy to join a call as required, though these days Monday 5pm is tricky, so apologies for not replying straight away... I may have to ask for a different time, if we have a call and if it's possible?

ddooley commented 3 years ago

Discussed on Monday June 21 call: Yes, lets have Allison join call and discuss integration of SWO and OBI ! Wondering about curation capabilities, instance vs class usage, especially around software versions, and OBO level sanctioning of this etc.

allysonlister commented 3 years ago

Thanks - sounds great! With a bit of planning I could make the standard time for the calls, or perhaps 12PM West Coast / 8PM UK time might work? Depends on everyone else :-) Looking forward to it.

bpeters42 commented 3 years ago

We have quite a few people on the call (10-30); it will be very hard to find another slot for the OBI group. But we can certainly plan ahead. Just let us know what Mondays could work for you. As long as they are not federal holidays, any date should be fine.

On Tue, Jun 22, 2021 at 1:45 AM Allyson Lister @.***> wrote:

Thanks - sounds great! With a bit of planning I could make the standard time for the calls, or perhaps 12PM West Coast / 8PM UK time might work? Depends on everyone else :-) Looking forward to it.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/obi-ontology/obi/issues/1175#issuecomment-865748870, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADJX2IXEFKEVH76EH2TMSE3TUBEQ5ANCNFSM4NTBLC5Q .

-- Bjoern Peters Professor La Jolla Institute for Immunology 9420 Athena Circle La Jolla, CA 92037, USA Tel: 858/752-6914 Fax: 858/752-6987 http://www.liai.org/pages/faculty-peters

allysonlister commented 3 years ago

Good morning! I'm unavailable on the 28th and you're not holding a call on the 5th, so how about if I join the July 12 call please?

Thanks!

bpeters42 commented 3 years ago

That should work great! Will take this off ticket, and respond on the obi mailing list.

On Wed, Jun 23, 2021 at 1:26 AM Allyson Lister @.***> wrote:

Good morning! I'm unavailable on the 28th and you're not holding a call on the 5th, so how about if I join the July 12 call please?

Thanks!

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-- Bjoern Peters Professor La Jolla Institute for Immunology 9420 Athena Circle La Jolla, CA 92037, USA Tel: 858/752-6914 Fax: 858/752-6987 http://www.liai.org/pages/faculty-peters

allysonlister commented 3 years ago

Thanks for a great call!

We decided that it was worth looking into the use of Robot Templates for SWO development, to aid in the ease of term submission and general development. We'll pick this up again in the Autumn to see where things are.

ddooley commented 2 years ago

Any followup on this, Allyson?

ddooley commented 2 years ago

OBI May 2 call: A reference to a software class allows for properties such as a version identifier (string). This allows for versions of a software without needing to create a class for each version. Then a software class's instance can have a version data item. Instances of a version identifier could form a database, but doesn't need to be in OBI.

SWO is an "OBOfication" of EDAM?

Damion will see if the above vision fits SWO curation. Issue SWO can't be merged logically.

(Same problem for sequencers).

ddooley commented 1 year ago

https://github.com/allysonlister/swo/issues/61 shows progress on getting SWO importable into OBI once SWO URI's are standardized. There is also a commitment by SWO to adopt the above OBI terms using a robot table; checking on SWO issue dedicated for this.

allysonlister commented 1 year ago

Thanks for pinging us here! Yes, we're very happy to add the software you're suggesting. Also note that I think all issues in https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1040 have been resolved.

ddooley commented 1 year ago

Ok, let me know if you need assistance with that. Any ETA?

allysonlister commented 1 year ago

Apologies, but I am on annual leave until mid April - might before the end of April be ok? Would normally be quicker, but for that reason :-)

cmungall commented 3 months ago

Any update here?

allysonlister commented 2 months ago

Yeah - sorry about that. Grant deadlines headed my way and it's still flagged as important in my to-do list... I'm away on hols for the next few weeks. I am sorry about the delay... thank you for being patient!