search_ggp

Search GGP IDs with keyword or Entrez Gene / Uniprot / GenBank ID. The ID can be used for further searches. The other families support Entrez Gene IDs directly if the family='entrez' parameter is used. However, this function can be used to map the Entrez Gene ID into a homologous family which allows expanding the search to similar genes found from other organisms.

Parameter	Mandatory	Value
term	Yes	string or id
family	Yes	{canonical, homologene, ensembl, egenomes, entrez}
searchType	No	{ggp, entrez, uniprot, genbank} Default: ggp. In canonical family only ggp is supported.

Example query: /api/v001/search_ggp/?term=mec1&family=canonical

fetch_direct_partners

Search GGPs that are interacting with the given GGP. fetch_direct_interactions provides detailed information about the interacting GGP pairs and should be used in conjunction with this function.

Parameter	Mandatory	Value
ggpId	Yes	id
family	Yes	{canonical, homologene, ensembl, egenomes, entrez}
type	No	{regulation, indirect_regulation, binding}
subType	No	{regulation, positive_regulation, negative_regulation}
direction	No	{forward, backward, both} Direction can be used for specifying the Cause-Theme relation of the GGPs. E.g. "GGP1 regulates GGP2" => type = regulation & direction = forward. Binding events are symmetric and direction is always 'both'. By default all choices are included.
rowStart	No	Numeric value. Default: 0
rowCount	No	Numeric value. Default: 10.
taxonomyFilter	No	Comma separated list of NCBI taxonomy IDs or organism names. Limits the result set to the given organisms.
negation	No	{1, 0} 1 -> only negated events, 0 -> only non-negated events, by default both are included.

Example query: /api/v001/fetch_direct_partners/?ggpId=3993&family=canonical&type=regulation&direction=forward

fetch_direct_interactions

Search different interactions between 2 given GGPs.

Parameter	Mandatory	Value
ggpId1	Yes	id
ggpId2	Yes	id
family	Yes	{canonical, homologene, ensembl, egenomes, entrez}
type	No	{regulation, indirect_regulation, binding}
subType	No	{regulation, positive_regulation, negative_regulation}
direction	No	{forward, backward, both} Direction can be used for specifying the Cause-Theme relation of the GGPs. E.g. "GGP1 regulates GGP2" => type = regulation & direction = forward. Binding events are symmetric and direction is always 'both'. By default all choices are included.
rowStart	No	Numeric value. Default: 0
rowCount	No	Numeric value. Default: 10.
output	No	{simple, inline, full}. Default: full. Affects the output format. Full output contains a list of event elements.
taxonomyFilter	No	Comma separated list of NCBI taxonomy IDs or organism names. Limits the result set to the given organisms.
negation	No	{1, 0} 1 -> only negated events, 0 -> only non-negated events, by default both are included.

Example queries:
/api/v001/fetch_direct_interactions/?ggpId1=3993&&ggpId2=2883&family=canonical&type=regulation&direction=forward

/api/v001/fetch_direct_interactions/?ggpId1=3993&&ggpId2=2883&family=canonical&type=regulation&direction=forward&output=simple

fetch_common_partners

Search GGPs that have pairwise interactions with both of the given GGPs. This function is useful for searching the indirect links between the given GGPs.

Parameter	Mandatory	Value
ggpId1	Yes	id
ggpId2	Yes	id
family	Yes	{canonical, homologene, ensembl, egenomes, entrez}
type	Yes	{binding, regulators, regulatees} These types include implicit direction of the interaction. E.g. regulators => Search GGPs which regulate both of the given GGPs.
rowStart	No	Numeric value. Default: 0
rowCount	No	Numeric value. Default: 10.

Example query: /api/v001/fetch_common_partners/?ggpId1=3993&ggpId2=2883&family=canonical&type=binding

fetch_events

Search events for the given GGP. This is mainly useful for searching unary events, but can be used for regulation and binding events as well. However, this function does not search GGPs from nested interactions, i.e. it may not return all possible regulation interactions for the given GGPs.

Parameter	Mandatory	Value
ggpId	Yes	id
ggpId2	No	id. Optional second GGP. Using this parameter will limit the search to events that contain both given GGPs, but does not specify the explicit pairwise interaction between the GGPs. Use fetch_direct_interactions or fetch_network for pairwise interactions.
family	Yes	{canonical, homologene, ensembl, egenomes, entrez}
type	Yes	{'regulations', 'regulation', 'positive_regulation', 'negative_regulation', 'binding', 'phosphorylation', 'localization', 'gene_expression', 'protein_catabolism', 'transcription', 'acetylation', 'methylation', 'hydroxylation', 'glycosylation', 'catalysis', 'dna_methylation', 'ubiquitination', 'dephosphorylation', 'dna_demethylation', 'phosphorylationepi', 'deglycosylation', 'deacetylation', 'deubiquitination', 'demethylation', 'dehydroxylation'} regulations is a special case which includes regulation, positive_regulation and negative_regulation
rowStart	No	Numeric value. Default: 0
rowCount	No	Numeric value. Default: 10.
output	No	{simple, inline, full}. Default: full. Affects the output format. Full output contains a list of event elements.
taxonomyFilter	No	Comma separated list of NCBI taxonomy IDs or organism names. Limits the result set to the given organisms.
negation	No	{1, 0} 1 -> only negated events, 0 -> only non-negated events, by default both are included.

Example query:
/api/v001/fetch_events/?ggpId=3993&family=canonical&type=regulation&taxonomyFilter=9606

fetch_network

Search all pairwise interactions for an arbitrarily long list of Entrez Gene IDs. Query results contain a list of link elements.

Parameter	Mandatory	Value
ggpIdList	Yes	List of comma separated Entrez Gene IDs.
family	Yes	{homologene, ensembl, egenomes, entrez}
negation	No	{1, 0} 1 -> only negated events, 0 -> only non-negated events, by default both are included.
speculation	No	{1, 0} 1 -> only speculated events, 0 -> only non-speculated events, by default both are included.

Example query:
/api/v001/fetch_network/?ggpIdList=854287,852307,854106,855828,850770,852306,852308,851572,854954&family=entrez

fetch_occurrences

Search occurrences for the given generalized event ID. Other search functions limit the amount of occurrences shown, this function can be used for showing all occurrences of a single generalized event. rowCount and rowStart parameters affect the occurrences listed in contrast to other functions which iterate over generalized events. Query results contain one event element.

Parameter	Mandatory	Value
eventId	Yes	Generalized event ID.
family	Yes	{canonical, homologene, ensembl, egenomes, entrez}
rowStart	No	Numeric value. Default: 0
rowCount	No	Numeric value. Default: 10.
output	No	{simple, inline, full}. Default: full. Affects the output format.
taxonomyFilter	No	Comma separated list of NCBI taxonomy IDs or organism names. Limits the result set to the given organisms.

Example query:
/api/v001/fetch_occurrences/?eventId=516627&family=entrez&rowStart=20

Each response contains a root element called queryresponse. The root element consists of queryinfo and queryresults elements. queryinfo stores meta data of the query, including used query parameters, result counts etc. queryresults element contains the actual result set. If the query is invalid, the queryresponse will include queryErrors element instead of the queryresult element. Each function description has an example query showing the full output format. The more complicated output elements are described below.

event

Field	Type	Description
id	attribute	Event ID in the given family.
averageConfidence	attribute	Average confidence of all occurrences.
description	element	Human-readable description of the event.
type	element	Type of the event. E.g. Positive_regulation.
pairwiseInteractions	element	List of pairwiseInteraction elements derived from this event.
occurrences	element	List of occurrence elements.

occurrence

Field	Type	Description
source	attribute	Source archive of the document. E.g. "Pubmed Central"
sourceId	attribute	Source ID of the document.
confidence	attribute	Confidence value of the occurrence.
sentence	element	The sentence including the given event occurrence.
type	element	Event type.
trigger	element	Trigger word of the event. This element has it's own attributes, offsetBeg and offsetEnd.
ggps	element	List of argument ggp elements. Each ggp element has attributes role, offsetBeg, offsetEnd, id (ID of the family level ggp), consensusName
nestedOccurrences	element	List of occurrence elements nested in the given event. Each nested occurrence has the same fields as the root occurrence, excluding sentence element.

pairwiseInteraction

Field	Type	Description
source	element	Source ggp of the pairwise interaction. Contains id and consensusName elements
target	element	Target ggp of the pairwise interaction. Contains id and consensusName elements
type	element	Coarse type of the interaction.
direction	element	Direction of the interaction. E.g. "Forward" indicates that the source ggp is affecting the target ggp. Note that pairwiseInteractions list may contain the same interaction twice, for both directions.

link

Field	Type	Description
source	element	Entrez Gene ID of the source GGP.
sourceName	element	Name of the source GGP.
target	element	Entrez Gene ID of the target GGP.
targetName	element	Name of the target GGP.
coarseType	element	Coarse type of the interaction. E.g. Regulation
refinedType	element	More detailed type of the interaction. E.g. Regulation of binding.
coarsePolarity	element	Polarity of the root event. Positive, Negative or neutral.
refinedPolarity	element	Interpretation of the polarity of the whole chain of nested events.
event	element	ID of the event this pairwise interaction originates from.
direction	element	Direction of the interaction.
averageConfidence	element	Average confidence of all occurrences.
negation	element	1 if the event appears in confirmative context, otherwise 0.
speculation	element	1 if the event appears in speculative context, otherwise 0.