search

globalbioticinteractions / scan

Symbiota Collections of Arthropods Network (SCAN) Registry
1 stars 0 forks source link

association type mapping #3

Open jhpoelen opened 5 years ago

jhpoelen commented 5 years ago

@seltmann @neilcobb some SCAN records appear to use the suggested DwC format for associatedTaxa in form "[association type]: [taxon name]"

That is a good thing! However, to integrate the interaction/association types, we need a consistent dictionary/taxonomy for interactionTypes . GloBI re-uses OBO Relation Ontology for this.

Please review/comment on the mappings I'd like to suggest for the encountered types:

[anacardiaceae] - no mapping, taxon name

[associated with] - map to interactsWith http://purl.obolibrary.org/obo/RO_0002437

[cactaceae] - no mapping, taxon name

[cupressaceae] - no mapping, taxon name

[euphorbiaceae] - no mapping, taxon name

[ex] - map to hasHost http://purl.obolibrary.org/obo/RO_0002454

[eza/zza 1] - no mapping, ?

[h] - map to hasHost http://purl.obolibrary.org/obo/RO_0002454

[host] - map to hasHost http://purl.obolibrary.org/obo/RO_0002454

[larrea] - no mapping, taxon name

[larval foodplant] - eats http://purl.obolibrary.org/obo/RO_0002470

[pinaceae] - no mapping, taxon name

[platanaceae] - no mapping, taxon name

[reared ex caenothus herbaceous recv] - no mapping, invalid format

[reared ex cercis canadensis lot] - no mapping, invalid format

[reared ex] - map to hasHost http://purl.obolibrary.org/obo/RO_0002454

seltmann commented 5 years ago

[anacardiaceae] - no mapping, taxon name https://www.gbif.org/species/2398

[associated with] - map to interactsWith http://purl.obolibrary.org/obo/RO_0002437 Agreed

[cactaceae] - no mapping, taxon name https://www.gbif.org/species/2519

[cupressaceae] - no mapping, taxon name https://www.gbif.org/species/8144

[euphorbiaceae] - no mapping, taxon name https://www.gbif.org/species/4691

[ex] - map to hasHost http://purl.obolibrary.org/obo/RO_0002454 Agreed, but may have some discussion on this term in the future

[eza/zza 1] - no mapping, ? Needs to be corrected, ie need to know institution and catalog numbers

[h] - map to hasHost http://purl.obolibrary.org/obo/RO_0002454 Not sure, ie need to know institution and catalog numbers

[host] - map to hasHost http://purl.obolibrary.org/obo/RO_0002454 Yes! What institution is doing it this way? Also would be helpful for me to know because they seem to be developing a nice method

[larrea] - no mapping, taxon name https://www.gbif.org/species/3189928

[larval foodplant] - eats http://purl.obolibrary.org/obo/RO_0002470 Agreed

[pinaceae] - no mapping, taxon name https://www.gbif.org/species/3925 All of the unknown taxon mappings so far have been at the family level. This will be very common in arthropods that it is mapped to higher taxonomy (like family)

[platanaceae] - no mapping, taxon name https://www.gbif.org/species/6693

[reared ex caenothus herbaceous recv] - no mapping, invalid format This is more complex because there is no relationship for reared from in RO and herbaceous is a state of plant Caenothus. Can you let me know the institution and catalog number? I can propose a solution, but I think this is one example of a relationship we can bring to RO

[reared ex cercis canadensis lot] - no mapping, invalid format Same as above, but not not sure on the meaning of lot in this context

[reared ex] - map to hasHost http://purl.obolibrary.org/obo/RO_0002454 hasHost works and is correct, but loosing the information about reared. Reared=TRUE?

This is great. I see this as being part of the active process and it is super helpful.