migs standard?

[bradfordcondon]

i like the idea of this module settings MIGs standards (or perhaps a child module).
https://www.ncbi.nlm.nih.gov/pubmed/18464787

http://rd-alliance.github.io/metadata-directory/standards/mibbi-minimum-information-biological-and-biomedical-investigations.html

http://wiki.gensc.org/index.php?title=MIGS/MIMS

[bradfordcondon]

https://docs.google.com/spreadsheets/d/16LldjTG_ch83OKSZP0rK6CqkjAxb5a5ohGVRsFAgQEk/edit?usp=sharing

standard copied to a spreadsheet. i note theres no ontology mapping obvious to the spreadsheet, and i dont think we can expect all these fields to exist in genbank...

[bradfordcondon]

the migs standard is included in the biomaterial properties we import from the API. That said tehse properties are not mapped to terms so i think it could be a cool initiative.

[mpoelchau]

As I understand it, the MIGS standard is used only if the submitter chooses it. The information then shows up in the 'Attributes' fields.

https://www.ncbi.nlm.nih.gov/biosample/docs/packages/
https://www.ncbi.nlm.nih.gov/biosample/docs/packages/MIGS.eu.4.0/

Are there terms outside the 'attributes' in BioSample that should map to MIGS terms?

[bradfordcondon]

no thats where they show up if that package is chosen. Im remarking that the MIGS metadata fields themselves arent mapped to ontology terms as far as im aware, which is why, ofr now, we are putting them in ncbi_properties:term_name.

[mpoelchau]

Ah okay. Thanks for clarifying.

[bradfordcondon]

so heres the attribute of the example migs biosample:
https://www.ncbi.nlm.nih.gov/biosample/SAMN02900669

<Attribute attribute_name="isolate" harmonized_name="isolate" display_name="isolate">Sampling mortality from South Scruggs Spring</Attribute>
      <Attribute attribute_name="collection_date" harmonized_name="collection_date" display_name="collection date">Oct-2013</Attribute>
      <Attribute attribute_name="env_biome" harmonized_name="env_broad_scale" display_name="broad-scale environmental context">Desert</Attribute>
      <Attribute attribute_name="env_feature" harmonized_name="env_local_scale" display_name="local-scale environmental context">Spring outflow</Attribute>
      <Attribute attribute_name="env_material" harmonized_name="env_medium" display_name="environmental medium">Water</Attribute>
      <Attribute attribute_name="estimated_size" harmonized_name="estimated_size" display_name="estimated size">1.6Gb</Attribute>
      <Attribute attribute_name="geo_loc_name" harmonized_name="geo_loc_name" display_name="geographic location">USA:Ash Meadows National Wildlife Refuge</Attribute>
      <Attribute attribute_name="isol_growth_condt" harmonized_name="isol_growth_condt" display_name="isolation and growth condition">Somatic</Attribute>
      <Attribute attribute_name="lat_lon" harmonized_name="lat_lon" display_name="latitude and longitude">36.43 N 116.3 W</Attribute>
      <Attribute attribute_name="num_replicons" harmonized_name="num_replicons" display_name="number of replicons">24</Attribute>
      <Attribute attribute_name="ploidy" harmonized_name="ploidy" display_name="ploidy">Diploid</Attribute>
      <Attribute attribute_name="propagation" harmonized_name="propagation" display_name="propagation">Sexual</Attribute>
      <Attribute attribute_name="biotic_relationship" harmonized_name="biotic_relationship" display_name="observed biotic relationship">free living</Attribute>
      <Attribute attribute_name="health_state" harmonized_name="health_state" display_name="health state">Deceased</Attribute>
      <Attribute attribute_name="sub_species" harmonized_name="sub_species" display_name="sub species">pectoralis</Attribute>

No term mappings in the XML.

Oddly enough, the descriptions of some these attributes references ontology terms. For example, heres the description of env_local_scale:
Add terms that identify environmental entities having causal influences upon the entity at time of sampling, multiple terms can be separated by pipes, e.g.: shoreline [ENVO:00000486]|intertidal zone [ENVO:00000316]

However, if i search for the machine name of the attribute itself in the referenced ontology ENVO, I get no results: http://www.ontobee.org/search?ontology=ENVO&keywords=env_local_scale&submit=Search+terms

Taken together, if mIGS has attributes mapped to properties, it isnt integrated into NCBI, and its not using the same machine names as the attributes for the property types.