Implement new Phenotypes data table on disease/phenotype profile page

[andrewhercules]

The new GraphQL API disease endpoint now exposes more phenotypes data. And so we can replace the current unordered list with a more comprehensive data table. Further details and spec TBC.

Example diseases with phenotypes: Cowden Syndrome, Noonan Syndrome, ulcerative colitis

[andrewhercules]

Data is now available from the development API branch - see sample query

Data table design

Can we please implement the following data table based on the design spec? Please note that the section title has changed to Clinical Signs and Symptoms.

Important note

Expand the number of entries in row.evidence as each entry should be in its own row. Please check sample query above for examples where row.evidence has multiple entries. Also check Orphanet_1934 for an example phenotype - Muscular hypotonia - with 11 evidence entries

Column content

Qualifier

• Display "NOT" if rows[x].evidence[y].qualifierNot == true otherwise the column will be blank

Phenotype

• Display the rows[x].phenotypeHPO.name value
• If rows[x].phenotypeEFO.id exists, use the ID to link the rows[x].phenotypeHPO.name value to the disease profile page
• Display a tool-tip called "Description:" with the rows[x].phenotypeHPO.description value

Phenotype ID

• Display the rows[x].phenotypeHPO.id value
• Link the rows[x].phenotypeHPO.id value to EBI OLS using identifers.org - https://www.identifiers.org/ols/ + rows[x].phenotypeHPO.id value
  • Note: the rows[x].phenotypeHPO.id value needs to be reformatted with the underscore replaced with a colon - so HP_0001558 becomes HP:0001558)

Aspect

• Display the rows[x].evidence[y].aspect value
• Display a tool-tip "Sub-ontology: P (Phenotypic abnormality), I (inheritance), C (onset and clinical course), M (clinical modifier)."

Frequency

• If rows[x].evidence[y].frequencyHPO exists, display rows[x].evidence[y].frequencyHPO.name value and link to EBI OLS using identifers.org - https://www.identifiers.org/ols/ + rows[x].evidence[y].frequencyHPO.id value
  • Note: the rows[x].evidence[y].frequencyHPO.id value needs to be reformatted with the underscore replaced with a colon - so HP_0040283 becomes HP:0040283)
• If rows[x].evidence[y].frequencyHPO is null, display "N/A"

Onset

• This field is an array - display as an unordered list with no bullet point
• Display the rows[x].evidence[y].onset[z].name value; however if there are no elements in the array, display "N/A"
• Link the rows[x].evidence[y].onset[z].name value to EBI OLS using identifers.org - https://www.identifiers.org/ols/ + rows[x].evidence[y].onset[z].id value
  • Note: the rows[x].evidence[y].onset[z].id value needs to be reformatted with the underscore replaced with a colon - so HP_0003623 becomes HP:0003623)
• To test, please query for Orphanet_178469 or Orphanet_666

Modifier

• This field is an array - display as an unordered list with no bullet point
• Display the rows[x].evidence[y].modifier[z].name value; however if there are no elements in the array, display "N/A"
• Link the rows[x].evidence[y].modifier[z].name value to EBI OLS using identifers.org - https://www.identifiers.org/ols/ + rows[x].evidence[y].modifier[z].id value
  • Note: the rows[x].evidence[y].modifier[z].id value needs to be reformatted with the underscore replaced with a colon - so HP_0012828 becomes HP:0012828)
• To test, please query for Orphanet_178469 or Orphanet_666

Sex

• Display the rows[x].evidence[y].modifier[z].sex value and format using the text-transform: capitalize; property to make the first letter capital uppercase
• If rows[x].evidence[y].modifier[z].sex value is null, display "N/A"
• To test, please query for Orphanet_68356 or EFO_0010646

Evidence

• Display the rows[x].evidence[y].evidenceType value
• Depending on the rows[x].evidence[y].evidenceType value, display a tool-tip as noted in the table below

Value returned by API	Tool tip text
IEA	Inferred from Electronic Annotations (IEA) are extracted by parsing the Clinical Features sections of the Online Mendelian Inheritance in Man resource
PCS	Published Clinical Study (PCS) are annotations extracted from articles in the medical literature with the PubMed ID of the published study (if available)
TAS	Traceable Author Statement (TAS) is used for information gleaned from knowledge bases such as OMIM or Orphanet that have derived the information from a published source

Source

• Display the rows[x].evidence[y].resource value

References

• This field is an array and there are three different references that may appear in this field: PubMed IDs (e.g. PMID:31587869), OMIM IDs (e.g. OMIM:618404), or Orphanet IDs (ORPHA:178469).
• Display the rows[x].evidence[y].references[z] value; however if there are no elements in the array, display "N/A" (e.g. Orphanet_68356)
• For entries prefixed by "PMID", parse the string to obtain the ID and link to Europe PMC
  • If the length of rows[x].evidence[y].references is > 1, use the drawer component used in other tables to show multiple publications
• For entries prefixed with either "OMIM" or "ORPHA", link to the HPO website using the following format - https://hpo.jax.org/app/browse/disease/ + rows[x].evidence[y].references[z] (e.g. ORPHA:178469)

QC checks

• Acroosteolysis dominant type - Orphanet_955
• ulcerative colitis - EFO_0000729
• Early infantile epileptic encephalopathy - Orphanet_1934

[andrewhercules]

@LucaFumis the spec is complete

@d0choa please review the spec above. I slightly adjusted the "References" column as the identifers.org link structure won't work due to the prefixes - instead we can link directly to the HPO website

[d0choa]

It looks fantastic. Thank you @andrewhercules

[d0choa]

@LucaFumis @andrewhercules The name of the widget was never updated. I would recommend changing the name to avoid confusion with "phenotypes" that show up in our disease profile pages.

More importantly, the sources need to be updated to HPO and MONDO as described in the spec.

[andrewhercules]

Noted - I've added to the feedback document for the next round of polish

[andrewhercules]

Ticket closed as work completed and merged into beta

Polish work will be captured in subsequent Beta Release polish ticket

[andrewhercules]

@LucaFumis for Integration Day tomorrow - 24 February - can we please make the following small adjustments?

1. Change the name of the detail view to "Clinical signs and symptoms"
2. Change the letter acronym to "CS"
3. Update the "Source: EFO" list to include
   • MONDO (https://mondo.monarchinitiative.org/)
   • HPO (https://hpo.jax.org/app/)

[LucaFumis]

Last requested changes were implemented for Integration day. Ticket can be closed, I imagine.

[andrewhercules]

Ticket closed as work completed and merged into main for Beta release