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mwalzer / elixir-metadata

materials and minutes to the elixir metadata implementation study
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CV selection #1

Open mwalzer opened 5 years ago

mwalzer commented 5 years ago

If we select a group of cv terms from various CV to describe the metadata, e.g. the place of each file in the study design, can we make http://people.binf.ku.dk/vzn529/eta/ work for us?

veitveit commented 5 years ago

I assume yes, depending on how the CV is organized (synonyms, ...). Do we have anybody with time and javascript skills to work on this?

mwalzer commented 5 years ago
drawing

loading person ...

mwalzer commented 5 years ago

would be nice though.

veitveit commented 5 years ago

There is an annotation wizard as part of the ISA Creator tool. It integrates controlled vocabularies and you can directly search for keywords in even multiple ontologies. It also takes into account synonyms and other fields. We need to test this software though. https://isa-tools.org/

proccaserra commented 5 years ago

@veitveit thx for the interest in ISA format and supporting tools. Besides ISAcreator (java standalone desktop tool), we also have devised under H2020 PhenoMeNal project (https://portal.phenomenal-h2020.eu/) an API (https://github.com/ISA-tools/isa-api) to create, validate, convert, curate ISA documents . These can be either serialized as Tab or JSON documents. ISAcreator and the ISA-API can be made aware of ISA configurations, which can carry a metadata profile, defining a set of ontologies and semantic resources to be accessed when editing ISA documents (e.g. PSI-MS for mass spectrometry related terminology or STATO (http://stato-ontology.org) for anything related to statistical methods/study design). On the issue of ISAconfigurations, we had an initial set of xml files specific to proteomics. Key to smooth loading is making sure the terms used in ISA Study Measurement Type and Technology Type (investigation file instance) match terms declared in the ISA configurations. We can follow up on the particular issue of CV use, configurations and annotation requirements.

I will expand on ISA-API and related Galaxy tools to create and deposit ISA document in another issue.

veitveit commented 5 years ago

@proccaserra Thanks for this very useful information! The API sounds like a very way to go for us.

We also devised a few ISA configurations for proteomics experiments, inspired by the ones already available. We plan to further specify them soon.

Find the now uploaded configurations here: https://github.com/mwalzer/elixir-metadata/tree/master/isa_configurations