DataHarmonizer
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cidgoh
A standardized browser-based spreadsheet editor and validator that can be run offline and locally, and which includes templates for SARS-CoV-2 and Monkeypox sampling data. This project, created by the...
LinkML has an ifabsent rule system: https://linkml.io/linkml-model/docs/ifabsent/. How should DataHarmonizer implement this?
See https://github.com/linkml/linkml-runtime/blob/a49927d45eb3584f85921fdba6d5c1cd75f54585/tests/test_utils/input/pattern-example.yaml and https://github.com/linkml/linkml/issues/176 for examples of regular expressions and string substitition from structured_pattern converted into compiled regular expression in pattern field. Python version of algorithm for string substitution at...
LinkML provides an id_prefixes attribute for slots. We could use this to require a user enters the link between a biosample and the [EMP500 project](https://www.ncbi.nlm.nih.gov/bioproject/686344) as `BIOPROJECT: PRJEB42019` by specifying...
Then during the build process the linkml.py script can reflect this in the menu.js menu data.
I had been using `source` in some of my LinkML inputs, but that resulted in broken interfaces, as DH seems to expect `source` to say something about select lists. Could...
Problem is one can't simply type "Missing" into a "sample collection date" field. One also has to add the ontology id formatted precisely, i.e. "Missing [GENEPIO:0001618]", in order for it...
This should be a good issue to monitor re converting patterns like "{float} {unit}" into regular expressions: https://github.com/GenomicsStandardsConsortium/mixs/issues/388
Examples appear as bulleted lists in the `linkml-datastructure` branch, right? Could that be applied to guidance, too? Or some other style to show key/value pairs for `see_also`s, minimum and maximum...
Currently, copy/paste in the DH is limited to 1000 rows. Can this be expanded so that users can copy larger sets of data from the DH to be pasted in...
