Gene Type and Profile

Hi Chunlei

On 25 May 2019, at 00:22, Chunlei Wu <cwu@scripps.edu<mailto:cwu@scripps.edu>> wrote:

[Note that I have reordered Chunlei’s original email to make it easier to respond]

Thanks Alasdair! Marking up Gene objects from MyGene.info<http://mygene.info/> API would be our target. At this point, the Gene type still misses a lot fields, which we can probably help.

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?

As you have hopefully seen on the mailing list, we are pushing a first set of types up for inclusion into schema.org<http://schema.org>. We would welcome your comments and feedback on them either on the mailing list or through the GitHub issue
https://github.com/BioSchemas/specifications/issues/321

Or specifically for Gene
https://github.com/BioSchemas/specifications/issues/317


With regard to new properties, it would be good to understand the search need for them. Again creating issues on the GitHub issue tracker is probably the best approach
https://github.com/BioSchemas/specifications/issues/


Whle we have a first release going forward, we anticipate the need to add more properties and types going forward.

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.

I don’t see a schema.org<http://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?)?

Thanks for asking this question, it highlights that we as a community need to urgently review our documentation as to how people can engage with us and what the appropriate process is and to update our governance documentation.

Certainly asking questions on the mailing list is a good starting point, as is creating issues on the issue tracker. These discussions should be centred around example markup and usage of the markup.

Once there is some agreement within the specific group then the (simplified) process would be:

  *   Add properties to the type if required, or even propose a new type. At this point it is probably easiest to directly involve me in that process.
  *   Revise the profile by:
     *   Creating a new copy of the relevant gSheet and increasing the version number by 0.1
     *   Making edits in the spreadsheet and tracking these changes as a summary list on the front sheet (we’re still developing the best practice on this)
     *   Running the GoWeb tool over the spreadsheet to generate the web version
     *   Creating a pull request on the website and communicating the changes to the community
  *   Deploy code on sites, or dev sites, so that we can verify that the approach works in practice

There is then the process of moving a draft profile to current, for which we are keen to see live deployments of the markup on sites.

Hopefully this helps clarify some of your questions.

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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