ccdhmodel
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cancerDHC
CRDC-H model in LinkML, developed by the Center for Cancer Data Harmonization (CCDH)
I don't know if this is a LinkML error or something specific to the CRDC-H model, so I will cross post an issue in linkml/linkml Run [`make all`](https://github.com/cancerDHC/example-data/blob/issue-27-codable-concept-notebooks/Makefile) from this...
For example, what URL represents the NCIt as a system?
The current root node is [Entity](https://cancerdhc.github.io/ccdhmodel/v1.1/Entity/). I think it would be advantageous to use Biolinks [Named Thing](https://biolink.github.io/biolink-model/docs/NamedThing) as the root. This allows for easier integration with Biolink and consistency across...
The model has many types of observation classes. E.g.: - AlcoholExposureObservation - CancerGradeObservation - HistologicalCompositionObservation etc. In scenarios like this, there is often an abstract parent class that the children...
In [Biolink](https://biolink.github.io/biolink-model/docs/QuantityValue) and [NMDC](https://microbiomedata.github.io/nmdc-schema/QuantityValue/#class-quantity-value) we use a `quantity value` class to represent quantitative information. In NMDC we have a general [attribute value](https://microbiomedata.github.io/nmdc-schema/AttributeValue/) class from which quantity values, text values, images...
We currently use a number of dummy prefixes in the CCDH model: ``` prefixes: linkml: https://w3id.org/linkml/ ccdh: https://example.org/ccdh/ NCIT: http://purl.obolibrary.org/obo/NCIT_ GDC: http://example.org/gdc/ PDC: http://example.org/pdc/ ICDC: http://example.org/icdc/ HTAN: http://example.org/htan/ ``` We...
The OWL API parser complains when trying to read `ccdhmodel.owl.ttl`: ``` jim (main)$ robot convert -i owl/ccdhmodel.owl.ttl -o ccdhmodel.ofn 2021-07-09 22:17:39,644 ERROR org.semanticweb.owlapi.rdf.rdfxml.parser.OWLRDFConsumer - Entity not properly recognized, missing triples...
Trying to run `make` I encounter this error: ``` ccdhmodel jim (main)$ make rm -rf target/docs mkdir -p target/docs pipenv install Creating a virtualenv for this project... Pipfile: /Users/jim/Documents/Source/ccdhmodel/Pipfile Using...
Most LinkML and CCDH software developers use computers running macOS. We should try setting it up and running it on a Windows computer, and documenting whether any additional steps are...