BioKB API Resources
Version: 1.0.0
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Table of Contents
Text Mining Hub resources
This API methods are the result of the Text-mining and semantic web technologies project developed during the Elixir-EU BioHackathon of 2019. For more details, please see the project report..
/tmh/getMentions/
GET
Summary
Returns a list of publications for a given list of entity IDs in which the entities appear.
Description
Returns a list of publications for a given list of entity IDs in which the entities appear.
Parameters
| Name |
Located in |
Description |
Required |
Schema |
| entity |
query |
entity as ontology code |
Yes |
[ string ] |
| limit |
query |
Limit number of results |
No |
integer |
| format |
query |
allows to choose a different format than JSON. For now, only cytoscape is available |
No |
string |
Responses
| Code |
Description |
| 200 |
List of publications |
| 400 |
bad input parameter |
/tmh/getCooccurrence/{entity}
GET
Summary
Returns a list of entities that co-appear together at publication level
Description
Returns a list of entities that co-appear together at publication level
Parameters
| Name |
Located in |
Description |
Required |
Schema |
| entity |
path |
Entity as ontology code |
Yes |
string |
| limit |
query |
Limit number of results |
No |
integer |
| format |
query |
allows to choose a different format than JSON. For now, only cytoscape is available |
No |
string |
| entity_types |
query |
list of entity types as ints |
No |
[ string ] |
Responses
| Code |
Description |
| 200 |
List of cooccurrences |
| 400 |
bad input parameter |
/tmh/bulk/getCooccurrence/
GET
Summary
bulk method for getCooccurrence
Description
Bulk operation to perform multiple requests to getCooccurrence. Supports POST too
Parameters
| Name |
Located in |
Description |
Required |
Schema |
| entity |
query |
entity as ontology code |
Yes |
[ string ] |
| limit |
query |
Limit number of results |
No |
integer |
| format |
query |
allows to choose a different format than JSON. For now, only cytoscape is available |
No |
string |
| entity_types |
query |
list of entity types as ints |
No |
[ string ] |
Responses
| Code |
Description |
| 200 |
Dictionary containing a map of entity codes to their corresponding list of cooccurrences |
| 400 |
bad input parameter |
BioKB resources
/api/entity_relationships_sentences/{entity}?limit={limit}&threshold={threshold}
GET
Summary
Retrieve entity relationships and sentences for a given entity in TSV format.
Description
Route to get entity relationships and sentences for a given entity.
The column count in the TSV file shows the number of occurrences of the given relationship in the sentence.
Parameters
| Name |
Located in |
Description |
Required |
Schema |
| entity |
path |
Entity as ontology code |
Yes |
string |
| limit |
query |
Number of entity relationships per direction (default 500) |
No |
number |
| threshold |
query |
Filter out entity relationships with a count lower or equal than threshold (default 0) |
No |
number |
Responses
| Code |
Description |
| 200 |
entities co-related to a given entity |
/api/entity_relationships_shortcut/{entity}/{direction}
/api/cooccurrences/{entity}
GET
Summary
Retrieve Cooccurrences for a given entity
Description
Route to get Cooccurrences for a given entity
Parameters
| Name |
Located in |
Description |
Required |
Schema |
| entity |
path |
Entity as ontology code |
Yes |
string |
Responses
| Code |
Description |
| 200 |
entities co-related to a given entity |
/api/entity_relationships_shortcut/{entity}/{direction}
GET
Summary
shortcut to retrieve entities related to a given entity
Description
Shortcut to get entities related to a given entity
Parameters
| Name |
Located in |
Description |
Required |
Schema |
| entity |
path |
Entity as ontology code |
Yes |
string |
| direction |
path |
relationship direction, either incoming or outgoing |
Yes |
string |
| type |
query |
Allows for type filtering. |
No |
[ string ] |
| relationship |
query |
Allows for relationship filtering. |
No |
[ string ] |
| start |
query |
For pagination. |
No |
integer |
| length |
query |
Limit the number of results. |
No |
integer |
Responses
| Code |
Description |
| 200 |
search entities related to a given entity |
| 400 |
bad input parameter |
Models
Publication
| Name |
Type |
Description |
Required |
| title |
string |
Example: "Macrolides beyond the conventional antimicrobials: a class of potent immunomodulators" |
No |
| year |
integer |
Example: 2008 |
No |
| journal_title |
string |
Example: "International Journal of Antimicrobial Agents" |
No |
| pmc_id |
string |
Example: "PMC4896250" |
No |
| pm_id |
string |
Example: 31832069 |
No |
| doi |
string |
Example: "10.1016/j.ijantimicag.2007.08.001" |
No |
| preprint_id |
string |
|
No |
| other_id |
string |
Example: "1c08baf0-bc3c-11e5-ac4e-001a4ae51246" |
No |
| id |
string |
|
No |
CoOccurrence_biokb
| Name |
Type |
Description |
Required |
| weight |
integer |
Example: 16839 |
No |
| entity_code |
string |
Example: "BTO:0000763" |
No |
| text |
string |
Example: "allergic rhinitis" |
No |
| type |
string |
Example: "Tissue" |
No |
| link |
string |
Example: "/cooccurrence/DOID:2841-DOID:4" |
No |
CoOccurrence
| Name |
Type |
Description |
Required |
| score |
integer |
Example: 673 |
No |
| info |
object |
|
No |
| resources |
[ string ] |
Example: ["BioKB","JensenLabService"] |
No |
RelationshipsResponse
| Name |
Type |
Description |
Required |
| draw |
integer |
Used for datatables. See https://datatables.net/manual/server-side |
No |
| column_occurrences |
object |
Used for YADTCF |
No |
| data |
[ object ] |
|
No |
| graph |
object |
|
No |
RelationshipItem
| Name |
Type |
Description |
Required |
| count |
integer |
Example: 24 |
Yes |
| relationship |
string |
Example: "bindsWith" |
Yes |
| relationship_uri |
string |
Example: "/relationship/ENSMUSP00000034588-bindsWith-ENSP00000363868" |
Yes |
| source |
string |
Example: "ABCA1" |
Yes |
| target_code_display |
string |
Example: "ENSMUSP00000034588" |
Yes |
| target_label |
string |
Example: "ciclosporin" |
Yes |
| target_type |
string |
Example: "Chemical" |
Yes |
| target_uri |
string |
Example: "http://lcsb.uni.lu/biokb/entities/CIDs05280754" |
Yes |
Graph
| Name |
Type |
Description |
Required |
| direction |
string |
Example: "incoming" |
Yes |
| nodes |
[ object ] |
|
Yes |
| edges |
[ object ] |
|
Yes |
GraphNode
| Name |
Type |
Description |
Required |
| code |
string |
Example: "ENSP00000363868" |
Yes |
| id |
string |
Example: "http://lcsb.uni.lu/biokb/entities/ENSP00000363868" |
Yes |
| label |
string |
Example: "ABCA1" |
Yes |
| type |
string |
Example: "protein" |
Yes |
GraphEdge
| Name |
Type |
Description |
Required |
| direction |
string |
Example: "incoming" |
Yes |
| from |
string |
Example: "http://lcsb.uni.lu/biokb/entities/ENSMUSP00000034588" |
Yes |
| to |
string |
Example: "http://lcsb.uni.lu/biokb/entities/ENSP00000363868" |
Yes |
| label |
string |
Example: "bindsWith" |
Yes |
| type |
string |
Example: "Protein" |
Yes |
| value |
integer |
Example: 23 |
Yes |