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HumanCellAtlas / ontology

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Display human (FMA) labels #56

Open dosumis opened 4 years ago

dosumis commented 4 years ago

HCAO is described as

Mammalian anatomy and cell type terms from Uberon and the cell ontology; Human-specific labels from the Foundational Model of Anatomy

HCAO pulls in FMA labels, (e.g. Hand in place of manus) but these are not displayed, except in an obscure place in term info:

image

Instead we should have:

image

Proposed implementation:

  1. Currently only the terms with an FMA xref get a prefLabel https://github.com/HumanCellAtlas/ontology/blob/master/src/sparql/construct_fma_labels.sparql We could generate a prefLabel for all (using Uberon label where there is no xref) - using uberon label where there's no xref to FMA.
  2. Alter https://github.com/HumanCellAtlas/ontology/blob/master/ols/ols-config.yaml to set label_property for HCAO to skos:prefLabel
dosumis commented 4 years ago

@henrietteharmse: Based on advice from @simonjupp that this was possible, I tried switching the AP used for label by adding this to the config:

label_property:  http://www.w3.org/2004/02/skos/core#prefLabel

The container builds and loads but this doesn't switch the display label as intended. There is no mention of this config setting in the developer doc here:

Would you be able to look into whether this configuration option is available and if so how it should be set and whether it works? Would it help if I set up a branch for testing?

dosumis commented 3 years ago

Postponed until HCA switches to using new containerised build OLS

dosumis commented 2 years ago

Low priority.