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IHEC / ihec-ecosystems

This repo is for code and documentation associated with the ihec-ecosystems working group
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Update of IHEC Metadata Specification #104

Open juettemann opened 4 years ago

juettemann commented 4 years ago

The specification page has not been updated in a while and does not reflect recent developments. It also still has the ambiguity with regard to the Molecule (linked to a date). Version 2.0 is missing completely.

https://github.com/IHEC/ihec-metadata/blob/master/specs/Ihec_metadata_specification.md

dzerbino commented 4 years ago

Hello @juettemann ,

I believe you got confused by the old repo, ihec-metadata, which is basically deprecated.

This repo is much more up-to-date: https://github.com/IHEC/ihec-ecosystems/tree/master/docs/metadata

Cheers,

Daniel

juettemann commented 4 years ago

Thanks @dzerbino, I indeed forgot about the v2.0 document.

If one starts at landing page https://github.com/IHEC/ihec-ecosystems and follows the link in the Metadata section, only v1.0 is visible: https://github.com/IHEC/ihec-ecosystems/blob/master/docs/metadata/1.0/Ihec_metadata_specification.md No link to v2.0. I will update the landing page and also link the v1.0/v2.0 documents to each other, unless there is a reason not to do so?

A couple of things: v1.0 Are we keeping the date in the specification: "MOLECULE or MOLECULE_ONTOLOGY_URI, in the experiment (or sample object for submissions prior to 2018)."

v1.0 & v2.0 "This document describes metadata elements extending the SRA XML Schema 1.2." Looking at the version of the schemas in https://github.com/IHEC/ihec-ecosystems/tree/master/schemas/xml

Their version ranges from 1.1 to 1.8, only one has 1.2. The v1.8 is most interesting as it seems 1.5.61 is the most recent one: https://github.com/enasequence/schema/tree/master/src/main/resources/uk/ac/ebi/ena/sra/schema

Is this variety intentional? Are these schemas updated?

Thanks, Thomas

dzerbino commented 4 years ago
  1. You're right, please update the URL
  2. Let's leave the date at present, it won't come back for a while ;)
  3. I have no idea about the variety of XML formats. Maybe @sitag knows something about this?
sitag commented 4 years ago

@dzerbino @juettemann EGA maintains a ftp with SRA xmls, I think the ftp links for xsd here: https://www.ebi.ac.uk/ena/submit/read-xml-format-1-4 I think there may be slightly differences from SRA.