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Indicate how should FALDO be used to indicate feature locations #210

Open cmungall opened 6 years ago

cmungall commented 6 years ago

I'm trying to understand the location model in bioschemas

In http://bioschemas.org/types/BioChemEntity/

I see we have a 'location' field, the values of which may be Place OR PostalAddress OR PropertyValue OR Text OR URL

I'm not sure what the use case for allowing postal addresses on genes is?

The notes says:

Schema: The location of for example where the event is happening, an organization is located, or where an action takes place. Bioschemas: The location can refer to a position in the chromosome or sequence or to a physical place where, for instance, a sample is stored. Using additionalType is advised to make the distinction. For instance, FALDO can be used for sequence coordinates. Note: The list of Expected Types has been extended as schema.org/location only has Place, PostalAddress and Text.

There is a bit ambiguous - exactly what FALDO class is expected here?

I can only find one example:

https://github.com/BioSchemas/specifications/blob/4e666e07f1c2c6ed0cacac81fb661d67a31f22b0/BioChemEntity/examples/example.json#L42-L46

The gene has position 837 - what does this mean?

I would recommend having this be more formally specified, with a BioChemEntity being equivalent to or a superclass of SO types, and faldo:location being mapped to bs:location, with a faldo:Region being the range.

cc @JervenBolleman

AlasdairGray commented 6 years ago

location is very much tied to geographical addresses.

From memory, I think the motivation was to allow location to be used in two different ways.

  1. To indicate where a biological sample could be retrieved from
  2. To indicate a region of a BioChemEntity

Personally I think that we should separate out these two uses as it leads to the confusion that is highlighted in this issue.

AlasdairGray commented 6 years ago

We are now proposing to split location in a structure from geographic location. The proposal is to use a new property for the location in a structure.

AlasdairGray commented 4 years ago

This no longer relates to BioChemEntity but to SequenceRange