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using BTE TRAPI endpoint for JSON tests #26

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Apr 7, 2021
Merged

using BTE TRAPI endpoint for JSON tests #26

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ad6736a
using BTE TRAPI endpoint for JSON tests
colleenXu Mar 23, 2021
28348da
correct smartapi key
colleenXu Mar 26, 2021
5ebac82
add changes, notes on current BTE TRAPI behavior with MyGene
colleenXu Mar 26, 2021
c6eb366
Merge branch 'main' into ServiceProvider_additions
colleenXu Apr 6, 2021
d3ca823
Merge branch 'SP_2' into ServiceProvider_additions
colleenXu Apr 6, 2021
ee84805
update urls, phenotype_of predicate for mydisease phenotypicFeature -…
colleenXu Apr 6, 2021
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4 changes: 2 additions & 2 deletions onehop/test_triples/KP/Service_Provider/MyChem.info_API.json
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@@ -1,6 +1,6 @@
{
"url": "https://smart-api.info/ui/8f08d1446e0bb9c2b323713ce83e2bd3",
"TRAPI": false,
"url": "https://api.bte.ncats.io/v1/smartapi/8f08d1446e0bb9c2b323713ce83e2bd3/query",
"TRAPI": true,
"edges": [
{
"subject_category": "biolink:ChemicalSubstance",
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16 changes: 8 additions & 8 deletions onehop/test_triples/KP/Service_Provider/MyGene.info_API.json
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@@ -1,6 +1,6 @@
{
"url": "https://smart-api.info/ui/59dce17363dce279d389100834e43648",
"TRAPI": false,
"url": "https://api.bte.ncats.io/v1/smartapi/59dce17363dce279d389100834e43648/query",
"TRAPI": true,
"edges": [
{
"subject_category": "biolink:Gene",
Expand All @@ -13,8 +13,8 @@
"subject_category": "biolink:MolecularActivity",
"object_category": "biolink:Gene",
"predicate": "biolink:enabled_by",
"subject": "GO:0046872",
"object": "NCBIGENE:10101"
"subject": "GO:0008147",
"object": "NCBIGENE:4256"
},
{
"subject_category": "biolink:Gene",
Expand All @@ -27,8 +27,8 @@
"subject_category": "biolink:BiologicalProcess",
"object_category": "biolink:Gene",
"predicate": "biolink:has_participant",
"subject": "GO:0002098",
"object": "NCBIGENE:285381"
"subject": "GO:0043610",
"object": "NCBIGENE:2475"
},
{
"subject_category": "biolink:Gene",
Expand All @@ -41,8 +41,8 @@
"subject_category": "biolink:CellularComponent",
"object_category": "biolink:Gene",
"predicate": "biolink:expresses",
"subject": "GO:0005654",
"object": "NCBIGENE:285381"
"subject": "GO:0033268",
"object": "NCBIGENE:6326"
},
{
"subject_category": "biolink:Gene",
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4 changes: 2 additions & 2 deletions onehop/test_triples/KP/Service_Provider/Ontology_Lookup_Service_API.json
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@@ -1,6 +1,6 @@
{
"url": "https://smart-api.info/ui/1c056ffc7ed0dd1229e71c4752239465",
"TRAPI": false,
"url": "https://api.bte.ncats.io/v1/smartapi/1c056ffc7ed0dd1229e71c4752239465/query",
"TRAPI": true,
"edges": [
{
"subject_category": "biolink:Disease",
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4 changes: 2 additions & 2 deletions onehop/test_triples/KP/Service_Provider/OpenTarget_API.json
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{
"url": "https://smart-api.info/ui/542ba165e1b4227854cf7c0a8addcc79",
"TRAPI": false,
"url": "https://api.bte.ncats.io/v1/smartapi/542ba165e1b4227854cf7c0a8addcc79/query",
"TRAPI": true,
"edges": [
{
"subject_category": "biolink:Gene",
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4 changes: 3 additions & 1 deletion onehop/test_triples/KP/Service_Provider/OpenTarget_README.md
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Expand Up @@ -10,4 +10,6 @@ parameters:
One of the answers should be EVEROLIMUS, which has
```
data.drug.id: "http://identifiers.org/chembl.compound/CHEMBL1908360"
```
```

Note: BTE TRAPI is currently having an issue. The raw output of this API is very redundant, and it seems that this is causing issues with the results section of the response (nodes and edges are fine).
4 changes: 1 addition & 3 deletions onehop/test_triples/KP/Service_Provider/README.md
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@@ -1,6 +1,4 @@
These KPs are not TRAPI APIs.

The tests described in the JSON files are written as-if these are TRAPI APIs. The expectation there is that a TRAPI query is made through BTE (the endpoint /v1/smartapi/{smartapi_id}/query) using the info in the JSON files. The edge to the "answer" node should have an attribute with the name "api" and value as the name of the API.
The JSON files assume that these APIs will be queried through BTE's TRAPI endpoint for querying individual SmartAPIs (accessible through the URLs provided).

Notes:
- tests are also described as queries that can be made directly to the API, in the additional README files. Notice that many API endpoints do not handle curies (ID prefixes) or predicates. The format of these queries is specified by the x-bte-annotated endpoint in the SmartAPI registry file.
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6 changes: 3 additions & 3 deletions onehop/test_triples/KP/Service_Provider/mydisease.info_API.json
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@@ -1,6 +1,6 @@
{
"url": "https://smart-api.info/ui/671b45c0301c8624abbd26ae78449ca2",
"TRAPI": false,
"url": "https://api.bte.ncats.io/v1/smartapi/671b45c0301c8624abbd26ae78449ca2/query",
"TRAPI": true,
"edges": [
{
"subject_category": "biolink:Disease",
Expand Down Expand Up @@ -47,7 +47,7 @@
{
"subject_category": "biolink:PhenotypicFeature",
"object_category": "biolink:Disease",
"predicate": "biolink:related_to",
"predicate": "biolink:phenotype_of",
"subject": "HP:0000224",
"object": "MONDO:0012107"
},
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33 changes: 16 additions & 17 deletions onehop/test_triples/KP/Service_Provider/mygene_README.md
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Expand Up @@ -12,18 +12,18 @@ go.MF.id: "GO:0046872"
```


2. For MolecularActivity -> Gene: Use the following info to query using the GO ID for metal ion binding
2. For MolecularActivity -> Gene: Use the following info to query using the GO ID for structural constituent of bone
```
fields: entrezgene
species: human
requestBody:
q: "GO:0046872"
q: "GO:0008147"
scopes: go.MF.id
size: 1000
```
One of the answers should be NUBP2, which has
One of the answers should be MGP, which has
```
entrezgene: 10101
entrezgene: 4256
```


Expand All @@ -41,18 +41,18 @@ go.BP.id: "GO:0002098"
```


4. For BiologicalProcess -> Gene: Use the following info to query using the GO ID for tRNA wobble uridine modification
4. For BiologicalProcess -> Gene: Use the following info to query using the GO ID for regulation of carbohydrate utilization
```
fields: entrezgene
species: human
requestBody:
q: "GO:0002098"
q: "GO:0043610"
scopes: go.BP.id
size: 1000
```
One of the answers should be DPH3, which has
One of the answers should be MTOR, which has
```
entrezgene: 285381
entrezgene: 2475
```


Expand All @@ -70,18 +70,18 @@ go.CC.id: "GO:0005654"
```


6. For CellularComponent -> Gene: Use the following info to query using the GO ID for nucleoplasm
6. For CellularComponent -> Gene: Use the following info to query using the GO ID for node of Ranvier
```
fields: entrezgene
species: human
requestBody:
q: "GO:0005654"
q: "GO:0033268"
scopes: go.CC.id
size: 1000
```
One of the answers should be DPH3, which has
One of the answers should be SCN2A, which has
```
entrezgene: 285381
entrezgene: 6326
```


Expand All @@ -100,7 +100,6 @@ pathway.reactome.id: "R-HSA-5358493"


8. For Pathway -> Gene: Use the following info to query using the REACT ID for Branched-chain amino acid catabolism
Note: The BTE TRAPI interface seems to have issues getting this result.
```
fields: entrezgene
species: human
Expand All @@ -115,7 +114,7 @@ entrezgene: 9673
```


9. For Gene -> Transcript: Use the following info to query using the ENSEMBL ID for KPNA5
9. For Gene -> Transcript: Use the following info to query using the ENSEMBL ID for KPNA5. Note BTE TRAPI endpoint for one API seems to have issues returning all of the expected results.
```
fields: ensembl.transcript
species: human
Expand All @@ -129,7 +128,7 @@ ensembl.transcript: ENST00000413340
```


9. For Gene -> Protein: Use the following info to query using the ENSEMBL ID for KPNA5
9. For Gene -> Protein: Use the following info to query using the ENSEMBL ID for KPNA5. Note BTE TRAPI endpoint for one API seems to have issues returning all of the expected results.
```
fields: ensembl.protein
species: human
Expand All @@ -144,7 +143,7 @@ ensembl.protein: ENSP00000396791


10. For Protein -> Gene: Use the following info to query using the UNIPROTKB ID for KPNA5
Note: The BTE TRAPI interface seems to have issues getting this result.
Note: The BTE TRAPI endpoint for one API is currently having issues successfully returning results.
```
fields: ensembl.gene
species: human
Expand All @@ -158,7 +157,7 @@ ensembl.gene: ENSG00000196911
```


11. For Gene -(homologous_to)-> Gene: Use the following info to query using the NCBIGENE ID for KCMF1
11. For Gene -(homologous_to)-> Gene: Use the following info to query using the NCBIGENE ID for KCMF1. The x-bte extension currently isn't written to do the inverse operation (MGI in mice -> NCBIGENE in humans).
```
fields: pantherdb.ortholog
requestBody:
Expand Down