VEP widget FE scoping

[buniello]

This ticket will include scoping iterations for the VEP widget on the variant page.

Please note that at time of issue opening, the variant index data/API is not completed e.g. the data team is working on adding new fields to capture distance info from VEP output. Also, we expect the majority of VEP widgets to consist of just one row.

Example of variant consequences API query

``` query { variant(variantId:"1_150556742_A_AG"){ transcriptConsequences { variantConsequences { id label } aminoAcidChange uniprotAccessions isEnsemblCanonical codons distance target { id approvedName } impact transcriptId lofteePrediction siftPrediction polyphenPrediction } } } ```

Example of variant consequences API response

``` { "data": { "variant": { "transcriptConsequences": [ { "variantConsequences": [ { "id": "SO:0001589", "label": "frameshift_variant" } ], "aminoAcidChange": "-567X", "uniprotAccessions": [ "Q6UY14" ], "isEnsemblCanonical": true, "codons": "-/G", "distance": null, "target": { "id": "ENSG00000143382", "approvedName": "ADAMTS like 4" }, "impact": "HIGH", "transcriptId": "ENST00000271643", "lofteePrediction": "HC", "siftPrediction": null, "polyphenPrediction": null }, { "variantConsequences": [ { "id": "SO:0001627", "label": "intron_variant" }, { "id": "SO:0001619", "label": "non_coding_transcript_variant" } ], "aminoAcidChange": null, "uniprotAccessions": [], "isEnsemblCanonical": true, "codons": null, "distance": null, "target": { "id": "ENSG00000237781", "approvedName": "ADAMTSL4 antisense RNA 2" }, "impact": "MODIFIER", "transcriptId": "ENST00000442435", "lofteePrediction": null, "siftPrediction": null, "polyphenPrediction": null }, { "variantConsequences": [ { "id": "SO:0001632", "label": "downstream_gene_variant" } ], "aminoAcidChange": null, "uniprotAccessions": [], "isEnsemblCanonical": true, "codons": null, "distance": 4728, "target": { "id": "ENSG00000264553", "approvedName": "microRNA 4257" }, "impact": "MODIFIER", "transcriptId": "ENST00000581735", "lofteePrediction": null, "siftPrediction": null, "polyphenPrediction": null }, { "variantConsequences": [ { "id": "SO:0001632", "label": "downstream_gene_variant" } ], "aminoAcidChange": null, "uniprotAccessions": [], "isEnsemblCanonical": true, "codons": null, "distance": 3459, "target": { "id": "ENSG00000203804", "approvedName": "ADAMTSL4 antisense RNA 1" }, "impact": "MODIFIER", "transcriptId": "ENST00000615012", "lofteePrediction": null, "siftPrediction": null, "polyphenPrediction": null }, { "variantConsequences": [ { "id": "SO:0001631", "label": "upstream_gene_variant" } ], "aminoAcidChange": null, "uniprotAccessions": [], "isEnsemblCanonical": true, "codons": null, "distance": 4723, "target": { "id": "ENSG00000289457", "approvedName": "novel transcript" }, "impact": "MODIFIER", "transcriptId": "ENST00000689641", "lofteePrediction": null, "siftPrediction": null, "polyphenPrediction": null } ] } } } ```

VEP Widget Subheader text: Variant consequence prediction for FIXED VARIANT ON PAGE Source: VEP

NOTE: please show / for null values

HORIZONTAL TABLE VERSION:

1. COLUMN HEADER: TRANSCRIPT (Tooltip: Ensembl canonical transcript) transcriptId — PLEASE NOTE: this field should be hyperlinked to Ensembl transcript page but don’t have enough info in data to build link
2. COLUMN HEADER: PREDICTED CONSEQUENCE - variantConsequences label resolved object hyperlinked to [http://purl.obolibrary.org/obo/`variantConsequencesId] (tooltip:impact`) — please note you could re-use VEP chip from ClinVar widget, where predicted consequence object is resolved by identifiers.org already
3. COLUMN HEADER: CONSEQUENCE SCORE - consequenceScore
4. COLUMN HEADER: GENE - approvedName within ‘target’ object hyperlinked to Platform page for targetId
5. COLUMN HEADER: AMMINOACID CHANGE aminoAcidChange
6. COLUMN HEADER: CODING CHANGE codons
7. COLUMN HEADER: DISTANCE FROM FOOTPRINT distanceFromFootprint (this field will be introduced with next data/API release)
8. COLUMN HEADER: DISTANCE FROM START SITE distanceFromTss (this field will be introduced with next data/API release)
9. COLUMN HEADER: LOFTEE PREDICTION - lofteePrediction
10. COLUMN HEADER: SIFT PREDICTION - siftPrediction
11. COLUMN HEADER: POLYPHEN PREDICTION - polyphenPrediction
12. UNIPROT ACCESSION: uniprotAccessions (can be more than one separated by comma) hyperlinked to https://www.uniprot.org/uniprotkb/uniprotAccessions

[d0choa]

While the new data is propagated, the current API column distance corresponds to the upcoming distanceFromFootprint. It can contain null values, but they will be replaced by 0 in the upcoming data. @DSuveges can provide more details if needed.

@buniello if I understood you well, the transcript link can be built like the next: http://www.ensembl.org/Homo_sapiens/Transcript/Summary?db=core;g=ENSG00000139618;t=ENST00000700199 We would get ENSG00000139618 from target.id and ENST00000700199 from transcriptId. Please confirm is this is what you were after.

Please keep using identifiers.org for sequence ontology and UniProt.

[d0choa]

Something important is that we will like this table to be sorted but after discussion with @DSuveges, we are still undecided on how to do it.

[buniello]

Thank you @d0choa, yes these are the links i was after. For table sorting, i kept that choice for later, not critical now

[buniello]

Comment on widget table sorting @gjmcn: a new field has been added to variant index dataset (and soon deployed in API) - transcriptIndex- , a non-nullable integer from 1 to the number of transcripts, where 1 is assigned to the most relevant relevant. This field should be used to order the genes in the VEP widget from most relevant and going down the list.

[buniello]

Pending: I decision on whether the two new transcript annotation fields, maneselect and appris should be presented to users in VEP widget and how (additional transcript annotation column similar to other resources)? Any feedback welcome

[d0choa]

Suggested changes in Aug 7th:

• [ ] Gene to be moved to the first column and replace content using approvedSymbol instead of approvedName
• [ ] Transcript information in a tooltip in the gene column. The tooltip could contain: "Ensembl canonical transcript: ENSTXXXXXX"
• [ ] Consequence score column can be removed as declared uninformative in the meeting
• [ ] Consider improve formatting of integer columns (Distances)
• [ ] Potentially save some width by playing with the headers

[buniello]

i agree with the suggested changes above

We should think about table sorting

[buniello]

note from Ellie:

• for the VEP widget, I’d like to see the gene column next to the transcript to be able to evaluate whether it is gene coding and thus understand the impact.

[d0choa]

Unless I'm missing something, the above comment requires no additional action @gjmcn