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RE: Outcomes of F2F Meeting

From: Chunlei Wu <cwu@scripps.edu>
Date: Wed, 8 May 2019 18:34:36 +0000
To: "Gray, Alasdair J G" <A.J.G.Gray@hw.ac.uk>, "public-bioschemas@w3.org" <public-bioschemas@w3.org>
CC: Kevin Xin <kevinxin@scripps.edu>
Message-ID: <BYAPR11MB3333DA5E858E22F7A1F90778B9320@BYAPR11MB3333.namprd11.prod.outlook.com>
Hi Alasdair,

           Thanks for the nice summary and the notes from the F2F meeting, very helpful for those who cannot be there.

           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. 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 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. Are these GitHub issues the good place to start with?

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

Best,

Chunlei

From: Gray, Alasdair J G<mailto:A.J.G.Gray@hw.ac.uk>
Sent: Wednesday, May 8, 2019 11:11 AM
To: public-bioschemas@w3.org<mailto:public-bioschemas@w3.org>
Subject: Outcomes of F2F Meeting

Hi All

We have had a very productive face-to-face meeting today making progress on the Bioschemas types and properties. Notes and outcomes have been captured in the agenda document
https://docs.google.com/document/d/1k5SVKreKbcuAzZ_Hp5YkMN6S1F2ROMHbjXNpdD5G4io/edit#<https://docs.google.com/document/d/1k5SVKreKbcuAzZ_Hp5YkMN6S1F2ROMHbjXNpdD5G4io/edit>

We are going to prepare a small set of types for pushing up to schema.org<http://schema.org> in a first wave of effort with further chunks of types pushed up in the following months. Based on the meeting today, we will be looking to push forward with

  *   BioChemEntity: as a top level type for all our Bioschemas work to keep these separated out in the schema.org<http://schema.org> hierarchy; this is partly to achieve the effect of the bio extension now that the extension mechanism is no more in schema.org<http://schema.org>
  *   BioChemStructure: renaming and generalisation of ProteinStructure
  *   BioSample: renaming Sample type proposal and focusing on life sciences
  *   DataRecord: a type to support the capturing of provenance information about a record separate from the content of the record, also avoiding everything being marked up as type Webpage
  *   Gene
  *   Protein
During the meeting today we agreed to hold back on SequenceAnnotation so that we can first do some markup with Gene and Protein. We can then reflect on the experience gained with these and then refine and evolve as our experience matures.

Obviously there are lots of types that we have been working on that were not represented by community members today. The choice of types to move forward with initially was purely on who was present at the meeting today. Other types that could be moved forward quite quickly includes the activities on Chemicals, Phenotype, Taxon, and others. If we can get activity pushing these forward then we can look to include them in the initial push to schema.org<http://schema.org>.

Thanks to everyone who was at the meeting today for working so hard and making it such as success.

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



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Received on Wednesday, 8 May 2019 19:21:28 UTC

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