Recent updates in Bioschemas

Dear Bioschemas Community,

There have been a lot of changes in Bioschemas in the last month with several key decisions made. Last week at the Biohackathon, we tried to follow through on the implications of these changes and decisions, but there is still more work to be done.

The main decision that has been made is to move from extending schema.org<http://schema.org> with a single BioChemEntity type which when used in a profile was additionally typed with classes from existing ontologies, to defining a schema.org<http://schema.org> extension consisting of types and properties for the major classes of resource (e.g. Dataset, Gene, Tool, etc) that we will be providing search for. Note that we are not attempting to reinvent the various life science ontologies that have been developed to model the domain. We are aiming to extend the schema.org<http://schema.org> vocabulary with the types needed to support searching for life sciences resources. The emphasis is on search, not accurate biological modelling. During the Biohackathon we made a start on defining these types and the properties that would be needed to support search. We would like the full Bioschemas community to be involved in this activity and ask that you review the proposal in the document at the following link. (Note that we have focused on the types for biological and chemical entities rather than the full spectrum of types, i.e. the document does not consider more generic types such as LabProtocol and Studies but these are not out of scope of Bioschemas and do need to be defined as well.)

https://docs.google.com/document/d/1_rO64r4JZgHA-66s_nsvLikUKZJnPJcwQte9BFb0WiU/edit?usp=sharing

Prior to the Biohackathon, the management committee approved updates to the following types:

  *   BioChemEntity v0.6: Inherits from Thing not Intangible

  *
Gene v0.1: Describing the sequence location was left as an open issue
  *
Protein v0.1: Describing the sequence location was left as an open issue
  *
Taxon v0.1:
  *
Sample v0.1

Based on these changes to the types, the following Profiles were updated and released:

  *   Gene v0.4

  *
Protein v0.5
  *
Sample v0.2
  *
Taxon v0.3

Note however that due to the discussions at the Biohackathon these types and profiles will be further revised in the coming months.

The management group decided to postpone the discussion on type and property mapping to existing ontologies. However, the discussion in Issue 227 (https://github.com/BioSchemas/specifications/issues/227) seems to have come to the consensus that skos mapping properties should be used. This will be a thread of work that needs to be completed after the types are more fully defined.

I will send a separate email summarising the outcomes of the Biohackathon*.

Best regards

Alasdair

*It has been a busy week catching up with the other parts of my job that did not get any attention last week

--
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

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