W3C home > Mailing lists > Public > public-bioschemas@w3.org > May 2019

RE: Outcomes of F2F Meeting

From: Chunlei Wu <cwu@scripps.edu>
Date: Fri, 24 May 2019 23:22:19 +0000
To: "Gray, Alasdair J G" <A.J.G.Gray@hw.ac.uk>
CC: "public-bioschemas@w3.org" <public-bioschemas@w3.org>, Kevin Xin <kevinxin@scripps.edu>
Message-ID: <BYAPR11MB3333B8B514C42336CEB294D6B9020@BYAPR11MB3333.namprd11.prod.outlook.com>
Thanks Alasdair! Marking up Gene objects from MyGene.info API would be our target. At this point, the Gene type still misses a lot fields, which we can probably help.

I looked into some existing documents to add a field to an existing type, but I’m still quite confused what the right process is.

For example, if I want to add “symbol” field to “Gene”, where is the place I can add and others can comment on whether it should be added or not?

I don’t see a schema.org definition file anywhere in GitHub repo (e.g. a JSON-LD file), then I went through some wiki documents, and located this folder for “Gene”:

https://drive.google.com/drive/u/1/folders/10Qf59xiMItW4c48jYh3S1LEd8cCFv0sW

Is it the right place? And which file I should use (0.3-draft or 0.4?)?

Chunlei

________________________________
From: Gray, Alasdair J G <A.J.G.Gray@hw.ac.uk>
Sent: Friday, May 24, 2019 7:43:04 AM
To: Chunlei Wu
Cc: public-bioschemas@w3.org; Kevin Xin
Subject: Re: Outcomes of F2F Meeting

Hi Chunlei

On 8 May 2019, at 19:34, Chunlei Wu <cwu@scripps.edu<mailto:cwu@scripps.edu>> wrote:

           I just added a “Gene” use case for our MyGene.info<https://mygene.info/> project to this doc<https://docs.google.com/document/d/1YI1JaQ5FwM9HJIFrEo7ECj5NwO-h6w9AYbAsPHUrYGE/edit> with some comments.

That is great. This has now been incorporated into the Gene use case on the Bioschemas website.
https://bioschemas.org/useCases/Gene/

MyGene.info<http://mygene.info/> provides a high performance gene-centric API. A typical gene object looks like this right now:

https://mygene.info/v3/1017

           MyGene.info<http://mygene.info/> API has been very well-used API resource in the community (~6M requests/m for ~10K unique IPs) We would be happy to work with this community to build up the Gene schema.

           Please advice how we (mostly Kevin Xin, cc’ed here, from my group and me) can help the process.

It would be great if you could try marking up your resource with the Gene type and help inform the discussion.

Are these GitHub issues the good place to start with?

https://github.com/BioSchemas/specifications/labels/type%3A%20Gene<https://github.com/BioSchemas/specifications/labels/type:%20Gene>

Yes these are the issues that we are looking to resolve.

Best regards

Alasdair


--
Alasdair J G Gray
Associate Professor in Computer Science,
School of Mathematical and Computer Sciences
Heriot-Watt University, Edinburgh, UK.

Email: A.J.G.Gray@hw.ac.uk<mailto:A.J.G.Gray@hw.ac.uk>
Web: http://www.macs.hw.ac.uk/~ajg33
ORCID: http://orcid.org/0000-0002-5711-4872
Office: Earl Mountbatten Building 1.39
Twitter: @gray_alasdair

To arrange a meeting: http://doodle.com/ajggray

________________________________

Heriot-Watt University is The Times & The Sunday Times International University of the Year 2018

Founded in 1821, Heriot-Watt is a leader in ideas and solutions. With campuses and students across the entire globe we span the world, delivering innovation and educational excellence in business, engineering, design and the physical, social and life sciences. This email is generated from the Heriot-Watt University Group, which includes:

  1.  Heriot-Watt University, a Scottish charity registered under number SC000278
  2.  Edinburgh Business School a Charity Registered in Scotland, SC026900. Edinburgh Business School is a company limited by guarantee, registered in Scotland with registered number SC173556 and registered office at Heriot-Watt University Finance Office, Riccarton, Currie, Midlothian, EH14 4AS
  3.  Heriot- Watt Services Limited (Oriam), Scotland's national performance centre for sport. Heriot-Watt Services Limited is a private limited company registered is Scotland with registered number SC271030 and registered office at Research & Enterprise Services Heriot-Watt University, Riccarton, Edinburgh, EH14 4AS.

The contents (including any attachments) are confidential. If you are not the intended recipient of this e-mail, any disclosure, copying, distribution or use of its contents is strictly prohibited, and you should please notify the sender immediately and then delete it (including any attachments) from your system.
Received on Friday, 24 May 2019 23:22:52 UTC

This archive was generated by hypermail 2.3.1 : Friday, 24 May 2019 23:22:54 UTC