January, 2020 Community Call - Kidney

Presenters:

Anna Greka - Broad Institute

Becky Steck - Michigan Medicine

Evren Azeloglu - Icahn School of Medicine at Mount Sinai

Slides:

Upcoming specific kidney area focus and scATACSeq, slide-seq, HCR/FISH, metabolomics, proteomics
Harmonising metadata, vocabulary & ontologies between initiatives (KPMP, HubMap, HCA) will help build the atlas
Strength of engaging directly with the clinicians, pathologists and researchers to address gaps, inconsistencies and errors in the ontologies
Modular approach to metadata structure design works well for the different data types in the project but had to de-modularise in order to simplify data re-use
Difficult to use the specifications defined in a spreadsheet to then validate incoming metadata
Important to engage all points of metadata collection early in the process

Way of harmonising metadata across consortia.
Need to understand important metadata fields from scATACSeq, slide-seq, HCR/FISH.
How to engage with reviewing and updating key ontologies such as UBERON and CL
Tools for how to define metadata schema
Generic validation tools that can be used with per consortium metadata schema

Given it is unlikely that we can conform to one united standard, can we build tools that allow interoperability/translation across all the standards? Are there fields that are “non-negotiable” across all the consortia?
- Can we have a standard interoperability format that would allow metadata translation?
- How do we ease the burden of how to map between standards? Are automated tools possible?
Improve communication with the ontology team or act as an intermediary between researchers/consortia and SPOT?
- More approachable web resources on how to provide feedback on ontologies
Can our json validator be used by anyone with schema as json? Is there adequate documentation to enable others to use it?