Evidence-labelled mTOR research: studies, entities, pathway claims, contradictions, open questions.
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Dataset version, corpus snapshot date, counts, evidence-code legend and how to cite the dataset. When the Atlas does not report the contested and conflicting counts itself, derived_counts adds them, computed from the relations, so they can be compared with find_contradictions.
This tool takes no arguments.
Dataset version, corpus snapshot date, counts, evidence-code legend and how to cite the dataset. When the Atlas does not report the contested and conflicting counts itself, derived_counts adds them, computed from the relations, so they can be compared with find_contradictions.
No arguments.
{
"type": "object",
"properties": {}
}Direct curated relations between two entities (either direction) with full cards for the supporting and conflicting studies. Answers questions such as "what is the evidence that A acts on B?". A study that repeats within the answer is sent in full once and afterwards as a short card with full_card_in.
| Argument | Type | Description |
|---|---|---|
| a* | string | |
| b* | string | |
| dedupe | boolean | Send a repeated study in full only once. Pass false for a full card every time. |
{
"type": "object",
"$schema": "http://json-schema.org/draft-07/schema#",
"required": [
"a",
"b"
],
"properties": {
"a": {
"type": "string"
},
"b": {
"type": "string"
},
"dedupe": {
"type": "boolean",
"default": true,
"description": "Send a repeated study in full only once. Pass false for a full card every time."
}
}
}Relations the Atlas marks as contested or that carry conflicting studies, with both sides of the evidence. status says which; breakdown splits the total. A contested relation with no conflicting study listed is flagged conflicting_studies_missing; relations named in its note or boundary are shown in named_in_text (a mention is not evidence). Paged: pass next_offset as offset for the rest. Optionally limited to one entity.
| Argument | Type | Description |
|---|---|---|
| brief | boolean | Shorten the long boundary and note text (text_truncated is set); get_relation has the full text. |
| limit | integer | Maximum 50; a larger value is capped at 50. |
| dedupe | boolean | Send a repeated study in full only once. Pass false for a full card every time. |
| entity | string | |
| offset | integer | For the next page: pass next_offset from the previous answer. |
| only_contested | boolean | Keep only relations the Atlas flags contested, not those that merely carry conflicting studies. |
{
"type": "object",
"$schema": "http://json-schema.org/draft-07/schema#",
"properties": {
"brief": {
"type": "boolean",
"default": false,
"description": "Shorten the long boundary and note text (text_truncated is set); get_relation has the full text."
},
"limit": {
"type": "integer",
"default": 20,
"maximum": 9007199254740991,
"minimum": 1,
"description": "Maximum 50; a larger value is capped at 50."
},
"dedupe": {
"type": "boolean",
"default": true,
"description": "Send a repeated study in full only once. Pass false for a full card every time."
},
"entity": {
"type": "string"
},
"offset": {
"type": "integer",
"default": 0,
"maximum": 9007199254740991,
"minimum": 0,
"description": "For the next page: pass next_offset from the previous answer."
},
"only_contested": {
"type": "boolean",
"default": false,
"description": "Keep only relations the Atlas flags contested, not those that merely carry conflicting studies."
}
}
}Signed, evidence-linked pathway relations (claims such as "Rheb activates mTORC1"). Filter by an entity on either end, by source/target, effect, contested status or minimum strength of the best supporting evidence.
| Argument | Type | Description |
|---|---|---|
| limit | integer | Maximum 50; a larger value is capped at 50. |
| effect | string | |
| entity | string | Entity on either end of the relation |
| offset | integer | For the next page: pass next_offset from the previous answer. |
| source | string | |
| target | string | |
| contested_only | boolean | Only relations marked contested or with conflicting studies |
| strongest_at_least | string | Keep relations whose best supporting study is at least this code in the order S > H > A > M |
{
"type": "object",
"$schema": "http://json-schema.org/draft-07/schema#",
"properties": {
"limit": {
"type": "integer",
"default": 20,
"maximum": 9007199254740991,
"minimum": 1,
"description": "Maximum 50; a larger value is capped at 50."
},
"effect": {
"enum": [
"activates",
"inhibits",
"binds",
"recruits",
"required-for",
"context-dependent",
"no-effect"
],
"type": "string"
},
"entity": {
"type": "string",
"description": "Entity on either end of the relation"
},
"offset": {
"type": "integer",
"default": 0,
"maximum": 9007199254740991,
"minimum": 0,
"description": "For the next page: pass next_offset from the previous answer."
},
"source": {
"type": "string"
},
"target": {
"type": "string"
},
"contested_only": {
"type": "boolean",
"description": "Only relations marked contested or with conflicting studies"
},
"strongest_at_least": {
"enum": [
"S",
"H",
"A",
"M",
"R",
"PP",
"RT"
],
"type": "string",
"description": "Keep relations whose best supporting study is at least this code in the order S > H > A > M"
}
}
}One profiled author by profile id ("claudio-de-virgilio"), full name, author-list form or ORCID: lab, role, profile URL and short cards of their studies in the Atlas.
| Argument | Type | Description |
|---|---|---|
| id | string | Alias of author. |
| author | string | e.g. "Claudio De Virgilio", "De Virgilio C", "claudio-de-virgilio" |
{
"type": "object",
"$schema": "http://json-schema.org/draft-07/schema#",
"properties": {
"id": {
"type": "string",
"description": "Alias of author."
},
"author": {
"type": "string",
"description": "e.g. \"Claudio De Virgilio\", \"De Virgilio C\", \"claudio-de-virgilio\""
}
}
}One entity (gene/protein, complex, drug, disease, process...) with its linked studies as short cards (first studies_limit) and every pathway relation it takes part in as a one-line claim. Accepts an id, a name or a synonym.
| Argument | Type | Description |
|---|---|---|
| id | string | Alias of entity. |
| entity | string | e.g. "mTORC1", "Rheb", "rapamycin" |
| studies_limit | integer | Maximum 50; a larger value is capped at 50. |
{
"type": "object",
"$schema": "http://json-schema.org/draft-07/schema#",
"properties": {
"id": {
"type": "string",
"description": "Alias of entity."
},
"entity": {
"type": "string",
"description": "e.g. \"mTORC1\", \"Rheb\", \"rapamycin\""
},
"studies_limit": {
"type": "integer",
"default": 25,
"maximum": 9007199254740991,
"minimum": 0,
"description": "Maximum 50; a larger value is capped at 50."
}
}
}One open or frontier question by ID (e.g. "H1", "F2"): the gap, what changed, what is still open, how it could be tested, linked studies.
| Argument | Type | Description |
|---|---|---|
| id* | string |
{
"type": "object",
"$schema": "http://json-schema.org/draft-07/schema#",
"required": [
"id"
],
"properties": {
"id": {
"type": "string"
}
}
}One pathway relation by ID (e.g. "RHEB-MTORC1"): mechanism, boundary conditions, confidence, supporting and conflicting studies.
| Argument | Type | Description |
|---|---|---|
| id* | string |
{
"type": "object",
"$schema": "http://json-schema.org/draft-07/schema#",
"required": [
"id"
],
"properties": {
"id": {
"type": "string"
}
}
}Full record for one study by Atlas ID (e.g. "SAB1994"), PMID, DOI or PMCID: abstract excerpt, extracted findings, linked entities, the relations it supports or contradicts, related open questions.
| Argument | Type | Description |
|---|---|---|
| id | string | Alias of sid. |
| sid | string | Atlas study ID ("SAB1994"), PMID ("23716719"), DOI or PMCID |
| study_id | string | Alias of sid. |
{
"type": "object",
"$schema": "http://json-schema.org/draft-07/schema#",
"properties": {
"id": {
"type": "string",
"description": "Alias of sid."
},
"sid": {
"type": "string",
"description": "Atlas study ID (\"SAB1994\"), PMID (\"23716719\"), DOI or PMCID"
},
"study_id": {
"type": "string",
"description": "Alias of sid."
}
}
}The Atlas's open questions (evidence gaps with testable hypotheses) and frontier questions. Paged. By default still_open is shortened at a sentence boundary (still_open_truncated); get_question has the full text, or pass brief=false.
| Argument | Type | Description |
|---|---|---|
| kind | string | |
| brief | boolean | Shorten still_open; false returns the full text. |
| limit | integer | Maximum 50; a larger value is capped at 50. |
| query | string | Keywords to find questions by their title, gap, hypothesis or what is still open, e.g. "rapamycin immune". |
| offset | integer | For the next page: pass next_offset from the previous answer. |
{
"type": "object",
"$schema": "http://json-schema.org/draft-07/schema#",
"properties": {
"kind": {
"enum": [
"open-question",
"frontier"
],
"type": "string"
},
"brief": {
"type": "boolean",
"default": true,
"description": "Shorten still_open; false returns the full text."
},
"limit": {
"type": "integer",
"default": 20,
"maximum": 9007199254740991,
"minimum": 1,
"description": "Maximum 50; a larger value is capped at 50."
},
"query": {
"type": "string",
"description": "Keywords to find questions by their title, gap, hypothesis or what is still open, e.g. \"rapamycin immune\"."
},
"offset": {
"type": "integer",
"default": 0,
"maximum": 9007199254740991,
"minimum": 0,
"description": "For the next page: pass next_offset from the previous answer."
}
}
}People in the Atlas by full name ("Claudio De Virgilio"), author-list form ("De Virgilio C"), ORCID or lab. results are authors with a profile page (full name, ORCID, lab, their study IDs); in_author_lists are matching names in study author lists without a profile.
| Argument | Type | Description |
|---|---|---|
| limit | integer | Maximum 50; a larger value is capped at 50. |
| query* | string | A name, ORCID or lab, e.g. "Sabatini", "Claudio De Virgilio", "Fribourg" |
| offset | integer | For the next page: pass next_offset from the previous answer. |
{
"type": "object",
"$schema": "http://json-schema.org/draft-07/schema#",
"required": [
"query"
],
"properties": {
"limit": {
"type": "integer",
"default": 20,
"maximum": 9007199254740991,
"minimum": 1,
"description": "Maximum 50; a larger value is capped at 50."
},
"query": {
"type": "string",
"description": "A name, ORCID or lab, e.g. \"Sabatini\", \"Claudio De Virgilio\", \"Fribourg\""
},
"offset": {
"type": "integer",
"default": 0,
"maximum": 9007199254740991,
"minimum": 0,
"description": "For the next page: pass next_offset from the previous answer."
}
}
}Find genes/proteins, complexes, drugs, diseases, processes, nutrients and outcomes by name or synonym. Each result says where it matched (match_field: name, synonym or description); use match="name" to leave out description-only hits.
| Argument | Type | Description |
|---|---|---|
| type | string | Optional type filter, e.g. "Drug", "Gene/Protein", "Disease" |
| limit | integer | Maximum 100; a larger value is capped at 100. |
| match | string | "any" also searches descriptions; "name" searches names and synonyms only. |
| query* | string | Name or synonym, e.g. "raptor", "sirolimus" |
| offset | integer | For the next page: pass next_offset from the previous answer. |
{
"type": "object",
"$schema": "http://json-schema.org/draft-07/schema#",
"required": [
"query"
],
"properties": {
"type": {
"type": "string",
"description": "Optional type filter, e.g. \"Drug\", \"Gene/Protein\", \"Disease\""
},
"limit": {
"type": "integer",
"default": 20,
"maximum": 9007199254740991,
"minimum": 1,
"description": "Maximum 100; a larger value is capped at 100."
},
"match": {
"enum": [
"any",
"name"
],
"type": "string",
"default": "any",
"description": "\"any\" also searches descriptions; \"name\" searches names and synonyms only."
},
"query": {
"type": "string",
"description": "Name or synonym, e.g. \"raptor\", \"sirolimus\""
},
"offset": {
"type": "integer",
"default": 0,
"maximum": 9007199254740991,
"minimum": 0,
"description": "For the next page: pass next_offset from the previous answer."
}
}
}Search the curated studies by keywords, optionally filtered by evidence code, a linked entity (gene, drug, disease...) and year range. Searches title, finding, authors (author-list form "Sabatini DM" and full names of profiled authors), PMID, DOI, PMCID, linked entities and their synonyms, journal, model system and the abstract excerpt. A query that is a PMID or DOI returns that study. Returns summary records with evidence codes and URLs.
| Argument | Type | Description |
|---|---|---|
| limit | integer | Maximum 50; a larger value is capped at 50. |
| query | string | Keywords, e.g. "rapamycin lifespan mice", a person ("Claudio De Virgilio"), a PMID or a DOI. Omit to list by filters only. |
| entity | string | Only studies linked to this entity (name, synonym or id), e.g. "Rheb". |
| offset | integer | For the next page: pass next_offset from the previous answer. |
| year_to | integer | |
| year_from | integer | |
| evidence_code | array | Keep only these evidence codes, e.g. ["H","S"] for human evidence. |
{
"type": "object",
"$schema": "http://json-schema.org/draft-07/schema#",
"properties": {
"limit": {
"type": "integer",
"default": 20,
"maximum": 9007199254740991,
"minimum": 1,
"description": "Maximum 50; a larger value is capped at 50."
},
"query": {
"type": "string",
"description": "Keywords, e.g. \"rapamycin lifespan mice\", a person (\"Claudio De Virgilio\"), a PMID or a DOI. Omit to list by filters only."
},
"entity": {
"type": "string",
"description": "Only studies linked to this entity (name, synonym or id), e.g. \"Rheb\"."
},
"offset": {
"type": "integer",
"default": 0,
"maximum": 9007199254740991,
"minimum": 0,
"description": "For the next page: pass next_offset from the previous answer."
},
"year_to": {
"type": "integer",
"maximum": 9007199254740991,
"minimum": -10000
},
"year_from": {
"type": "integer",
"maximum": 9007199254740991,
"minimum": -10000
},
"evidence_code": {
"type": "array",
"items": {
"enum": [
"S",
"H",
"A",
"M",
"R",
"PP",
"RT"
],
"type": "string"
},
"description": "Keep only these evidence codes, e.g. [\"H\",\"S\"] for human evidence."
}
}
}