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stringApp Automation Documentation

stringApp version 2.0.1

Last update: 2023-02-20

List of commands

Network query

Modify existing network

Visual properties

Functional enrichment

Other

Protein query

string protein query

The protein query retrieves a STRING network for one or more proteins. STRING is a database of known and predicted protein interactions for thousands of organisms, which are integrated from several sources, scored, and transferred across orthologs.

Arguments

  • cutoff (optional) Double Default: 0.4

    The confidence score reflects the cumulated evidence that this interaction exists. Only interactions with scores greater than this cutoff will be returned. It must be a value between 0.0 and 1.0.

  • includesViruses (optional) boolean Default: true

    By default, a query will search for identifiers in both the protein and virus databases. By changing this to false, only the protein database will be searched.

  • limit (optional) int Default: 10

    The maximum number of proteins to return in addition to the query set. It must be a value between 0 and 10000.

  • networkType (optional) String Default: full STRING network

    By default, the query will retrieve functional associations from STRING, but it can be set to physical interactions by setting this option to physical subnetwork.

  • newNetName (optional) String

    Name for the network to be created.

  • query required String

    Comma separated list of protein names or identifiers.

  • species (optional) String Default: Homo sapiens

    Species name. This should be the actual taxonomic name (e.g. homo sapiens, not human).

  • taxonID (optional) int Default: 9606

    The species taxonomy ID. See the NCBI taxonomy home page for IDs. If both species and taxonID are set to a different species, the taxonID has priority.

Example

string protein query query="cdk1"

Creates a STRING network of cdk1 and its first 10 neighbors in human (limit is equal to 10 and species to human by default).

List of commands - List of Network query commands

Compound query

string compound query

The compound query retrieves a STITCH network for one or more proteins or compounds. STITCH is a resource to explore known and predicted interactions of chemicals and proteins. Chemicals are linked to other chemicals and proteins by evidence derived from experiments, databases and the literature.

Arguments

  • cutoff (optional) Double Default: 0.4

    The confidence score reflects the cumulated evidence that this interaction exists. Only interactions with scores greater than this cutoff will be returned. It must be a value between 0.0 and 1.0.

  • includesViruses (optional) boolean Default: true

    By default, a query will search for identifiers in both the protein and virus databases. By changing this to false, only the protein database will be searched.

  • limit (optional) int Default: 10

    The maximum number of proteins and compounds to return in addition to the query set. It must be a value between 0 and 10000.

  • networkType (optional) String Default: full STRING network

    By default, the query will retrieve functional associations from STRING, but it can be set to physical interactions by setting this option to physical subnetwork.

  • newNetName (optional) String

    Name for the network to be created.

  • query required String

    Comma separated list of protein or compound names or identifiers.

  • species (optional) String Default: Homo sapiens

    Species name. This should be the actual taxonomic name (e.g. homo sapiens, not human).

  • taxonID (optional) int Default: 9606

    The species taxonomy ID. See the NCBI taxonomy home page for IDs. If both species and taxonID are set to a different species, the taxonID has priority.

Example

string compound query query="aspirin"

Creates a STITCH network of aspirin and its first 10 neighbors in human (the default values are used for both species and number of interactors), whereas the neighbors could be both proteins and compounds.

List of commands - List of Network query commands

Disease query

string disease query

The disease query retrieves a STRING network for the top-N human proteins associated with the queried disease in the DISEASES database. DISEASES is a weekly updated web resource that integrates evidence on disease-gene associations from automatic text mining, manually curated literature, cancer mutation data, and genome-wide association studies. STRING is a database of known and predicted protein interactions for thousands of organisms, which are integrated from several sources, scored, and transferred across orthologs.

Arguments

  • cutoff (optional) Double Default: 0.4

    The confidence score reflects the cumulated evidence that this interaction exists. Only interactions with scores greater than this cutoff will be returned. It must be a value between 0.0 and 1.0.

  • disease required String

    The name (or partial name) of a disease.

  • limit (optional) int Default: 100

    The maximum number of proteins to return in addition to the query set. It must be a value between 0 and 10000.

  • networkType (optional) String Default: full STRING network

    By default, the query will retrieve functional associations from STRING, but it can be set to physical interactions by setting this option to physical subnetwork.

  • species (optional) String Default: Homo sapiens

    Species name. This should be the actual taxonomic name (e.g. homo sapiens, not human).

  • taxonID (optional) int Default: 9606

    The species taxonomy ID. See the NCBI taxonomy home page for IDs. If both species and taxonID are set to a different species, the taxonID has priority.

Example

string disease query disease="Alzheimer's disease" limit=10

Creates a STRING network of the 10 proteins with highest integrated disease score for Alzheimer's disease according to DISEASES.

List of commands - List of Network query commands

PubMed query

string pubmed query

The PubMed query retrieves a STRING network of the top-N proteins pertaining to any topic of interest based on text mining of PubMed abstracts. STRING is a database of known and predicted protein interactions for thousands of organisms, which are integrated from several sources, scored, and transferred across orthologs.

Arguments

  • cutoff (optional) Double Default: 0.4

    The confidence score reflects the cumulated evidence that this interaction exists. Only interactions with scores greater than this cutoff will be returned. It must be a value between 0.0 and 1.0.

  • networkType (optional) String Default: full STRING network

    By default, the query will retrieve functional associations from STRING, but it can be set to physical interactions by setting this option to physical subnetwork.

  • limit (optional) int Default: 100

    The maximum number of proteins to return in addition to the query set. It must be a value between 0 and 10000.

  • pubmed required String

    Enter a pubmed query (see NCBI tutorials for information about pubmed query syntax).

  • species (optional) String Default: Homo sapiens

    Species name. This should be the actual taxonomic name (e.g. homo sapiens, not human).

  • taxonID (optional) int Default: 9606

    The species taxonomy ID. See the NCBI taxonomy home page for IDs. If both species and taxonID are set to a different species, the taxonID has priority.

Example

string pubmed query pubmed="Alzheimer's disease" limit=10

Creates a network of the top 10 proteins associated with Alzheimer's diseasse according to PubMed abstracts.

List of commands - List of Network query commands

Stringify network

string stringify

Creates a new network from the nodes and edges of the specified network by querying STRING for all of the nodes and then copying over the edges from the original network. In the resulting network, all nodes contain the typical information for a STRING network and the Change confidence command can be used to add STRING edges above a given confidence cutoff to the network.

Arguments

  • column required String Default: name

    Select the column to use to query for STRING nodes.

  • cutoff (optional) Double Default: 1.0

    The confidence score reflects the cumulated evidence that this interaction exists. Only interactions with scores greater than this cutoff will be returned. It must be a value betwene 0.0 and 1.0.

  • type (optional) String Default: full STRING network

    Type of the STRING interactions (edges) to be included in the network, either functional associations or physical interactions.

  • includeNotMapped (optional) boolean Default: true

    Option for choosing whether nodes that cannot be mapped to STRING identifiers should be included in the new network or not.

  • compoundQuery (optional) boolean Default: false

    Option for considering compounds when resolving the node identifiers and consequently querying STITCH instead of STRING.

  • networkNoGui required String Default: current

    Specifies a network by name, or by SUID if the prefix SUID: is used. The keyword CURRENT, or a blank value can also be used to specify the current network.

  • species required String Default: Homo sapiens

Example

string stringify column="name" networkNoGui="current" species="Homo sapiens"

Creates a STRING network from the nodes and edges of the current network by querying STRING with the human (Homo sapiens) protein names/identifiers contained in the name column.

List of commands - List of Network query commands

Expand network

string expand

Expands an already existing STRING network by more interactors such as STITCH compounds, proteins of the network species as well as proteins interacting with available viruses or host species proteins.

Arguments

  • additionalNodes (optional) int Default: 10

    The maximum number of proteins to return in addition to the nodes in the existing network.

  • network required String Default: current

    Specifies a network by name, or by SUID if the prefix SUID: is used. The keyword CURRENT, or a blank value can also be used to specify the current network.

  • nodeTypes (optional) String Default: STITCH compounds

    Type of interactors to expand the network by, including STITCH compounds (default choice), proteins of the same species as the network's one or other species for which host-virus interactions are available. Proteins are specified by the species name, for example, Homo sapiens for human proteins or Influenza A virus for influenza A proteins.

  • selectivityAlpha (optional) Double Default: 0.5

    The selectivity parameter provides a tradeoff between the specificity and the confidence of new interactors and must be a value between 0.0 and 1.0. Low selectivity will retrieve more hub proteins, which may have many high-confidence interactions to the current network but also many other interactions. High selectivity will retrieve proteins that primarily interact with the current network but with lower confidence, since the higher-confidence hubs have been filtered out.

Example

string expand network=current nodeTypes="Homo sapiens"

Expands the current network by further 10 human (Homo sapiens) proteins. If less than 10 new proteins are added to the network, this means that there were only that many available given the confidence cutoff of the network.

List of commands - List of Modify existing network commands

Change confidence

string change confidence

Changes the confidence of the network. If increased, the edges with a confidence score below the chosen cutoff will disappear. If decreased, new edges might be added to the network.

Arguments

  • confidence required Double Default: 0.4

    Confidence score for the STRING interactions to be included in this network. It must be a value between 0.0 and 1.0.

  • network required String Default: current

    Specifies a network by name, or by SUID if the prefix SUID: is used. The keyword CURRENT, or a blank value can also be used to specify the current network.

Example

string change confidence network="current" confidence=0.7

Requires all edges in the current network to have a confidence score equal or above 0.7. If the confidence cutoff for the network has been 0.4, some edges might disappear. On the other hand, if the cutoff has been higher, new edges might be added to the network.

List of commands - List of Modify existing network commands

Change network type

  • string change type

Changes the type of the network between functional associations (full STRING network) and physical interactions (physical subnetwork).

Arguments

  • type required String Default: full STRING network

    Type of the STRING interactions (edges) to be included in the network, either functional associations or physical interactions.

  • confidence (optional) Double Default: 0.4

    Confidence score for the STRING interactions to be included in this network. It must be a value between 0.0 and 1.0.

  • network required String Default: current

    Specifies a network by name, or by SUID if the prefix SUID: is used. The keyword CURRENT, or a blank value can also be used to specify the current network.

Example

string change type network="current" type="physical subnetwork"

All functional association edges in the current network will be replaced by physical interactions with a confidence score above the one of the current network. If the current network is already a physical subnetwork, nothing will happen.

List of commands - List of Modify existing network commands

Add nodes

string add nodes

Adds a new set of query nodes to an existing STRING network as well as their interactions with the nodes in the existing network.

Arguments

  • cutoff (optional) Double Default: 0.4

    The confidence score reflects the cumulated evidence that this interaction exists. Only interactions with scores greater than this cutoff will be returned. It must be a value between 0.0 and 1.0.

  • includesViruses (optional) boolean Default: true

    By default, a query will search for identifiers in both the protein and virus databases. By changing this to false, only the protein database will be searched.

  • limit (optional) int Default: 10

    The maximum number of proteins to return in addition to the query set. It must be a value between 0 and 10000.

  • network (optional) String Default: current

    Specifies a network by name, or by SUID if the prefix SUID: is used. The keyword CURRENT, or a blank value can also be used to specify the current network.

  • query required String

    Comma separated list of protein names or identifiers.

  • species (optional) String Default: Homo sapiens

    Species name. This should be the actual taxonomic name (e.g. homo sapiens, not human).

  • taxonID (optional) int Default: 9606

    The species taxonomy ID. See the NCBI taxonomy home page for IDs. If both species and taxonID are set to a different species, the taxonID has priority.

Example

string add nodes query="cdk1"

Adds cdk1 and its interaction edges to any proteins in the current network.

List of commands - List of Modify existing network commands

Make STRING network

string make string

Sets the network as a STRING network recognizable by the stringApp. This assumes that the network was originally derived from STRING and has all of the necessary STRING columns.

Arguments

  • network (optional) String Default: current

    Specifies a network by name, or by SUID if the prefix SUID: is used. The keyword CURRENT, or a blank value can also be used to specify the current network.

List of commands - List of Modify existing network commands

Show structure images

string show images

Shows or hides the structure images on the nodes.

List of commands - List of Visual properties commands

Show STRING style labels

string show labels

Shows or hides the STRING style labels on the nodes.

List of commands - List of Visual properties commands

Enable glass ball effect

string enable glass

Enables or disables the glass ball effect on the nodes.

List of commands - List of Visual properties commands

Retrieve functional enrichment

string retrieve enrichment

Retrieves the functional enrichment for the current STRING network. This includes enrichment for GO Biological Process, GO Cellular Component, GO Molecular Function, KEGG & Reactome Pathways, UniProt keywords, InterPro, PFAM, and SMART protein domains as well as STRING clusters. Note that in order to view the results, the command Show enrichment panel should be used in addition this this one.

Arguments

  • allNetSpecies (optional) String

    Specify the species, for which enrichment should be run in case of several species in the same network (e.g. virus-host networks).

  • background (optional) String Default: genome

    Another STRING network to be used as the background set for the functional ernichment. By default, the whole genome of the chosen species is considered.

  • selectedNodesOnly (optional) boolean Default: false

    Setting this to true and selecting a subset of the nodes will retrieve enrichment only for the selected nodes. If this is false enrichment will be retrieved for all nodes in the network

Example

string retrieve enrichment selectedNodesOnly=true

Retrieves functional enrichment for a set of selected nodes in the current network.

List of commands - List of Functional enrichment commands

Show enrichment panel

string show enrichment

Shows or hides the enrichment panel.

List of commands - List of Functional enrichment commands

Filter functional enrichment

string filter enrichment

Filters the terms in the enrichment table.

Arguments

  • categories (optional) String

Select the enrichment categories to show in the table. Possible values are:

  • GO Process: Gene Ontology Biological Process

  • GO Component: Gene Ontology Cellular Component

  • GO Function: Gene Ontology Molecular Function

  • InterPro Domains: Protein domains from InterPro

  • KEGG Pathways: KEGG pathways

  • PFAM Domains: Protein domains from PFAM

  • Reactome Pathways: Reactome pathways

  • STRING Clusters: CLusters of proteins in the STRING network with a specific functional annotation

  • SMART Domains: Protein domains from SMART

  • UniProt Keywords: Functional annotations from UniProt

  • overlapCutoff (optional) Double Default: 0.5

This is the maximum Jaccard similarity between annotation terms that will be allowed to keep a term with a lower FDR value than an already selected one. For paier of term with Jaccard similarity larger than this cutoff, the term from the pair with lower FDR will be excluded.

  • removeOverlapping (optional) boolean Default: false

Removes terms, whose enriched genes significantly overlap with already selected terms. Terms are ranked based on their FDR value.

Example

string filter enrichment categories="GO Process,KEGG Pathways" removeOverlapping=true

Filters the enrichment table to only show terms from the categories: GO Process and KEGG Pathways. This command also removes redundant terms with a Jaccard overlap larger than the default 50% (0.5)

List of commands - List of Functional enrichment commands

Show enrichment charts

string show charts

Shows the enrichment charts using the default settings (see Settings).

List of commands - List of Functional enrichment commands

Hide enrichment charts

string hide charts

Hides the enrichment charts.

List of commands - List of Functional enrichment commands

##Retrieve enriched publications

string retrieve publications

Retrieves the enriched PubMed publications for the current STRING network. In this case, each publication is represented by a set of genes recognized in it by text mining and this set of genes is tested for overrepresentation. Note that in order to view the results, the command Show publications panel should be used after this one.

Arguments

  • allNetSpecies (optional) String

    Specify the species, for which enrichment should be run in case of several species in the same network (e.g. virus-host networks).

  • background (optional) String Default: genome

    Another STRING network to be used as the background set for the publication ernichment. By default, the whole genome of the chosen species is considered.

  • selectedNodesOnly (optional) boolean Default: false

    Setting this to true and selecting a subset of the nodes will retrieve enrichment only for the selected nodes. If this is false enrichment will be retrieved for all nodes in the network

Example

string retrieve publications selectedNodesOnly=true

Retrieves enriched publications for a set of selected nodes in the current network.

List of commands - List of Functional enrichment commands

Show publications panel

string show publications

Shows or hides the enriched publications panel.

List of commands - List of Functional enrichment commands

Settings

string settings

Adjusts various default settings of the stringApp for network queries, enrichment retrieval and visual properties.

Arguments

  • additionalProteins (optional) int Default: 0

    Default number of additional interactors for the protein and compound query. It must be a number between 0 and 100.

  • chartType (optional) String Default: Split donut

    Set the desired chart type for enrichment visualization. Each chosen term is represented by a colored slice if it annotates the node and by a white/transparent slice if it does not. Possible chart types are:

    • Split donut: Each slice represents one of the visualized terms and is colored if the term annotates the node and white otherwise.
    • Donut slices only: Each slice represents one of the visualized terms and is colored if the term annotates the node and transparent otherwise.
    • Full donut: Each slice represents one of the visualized terms that annotate the node.
    • Split Pie Chart: Each slice represents one of the visualized terms and is colored if the term annotates the node and white otherwise.
    • Pie Chart: Each slice represents one of the visualized terms that annotate the node.

  • defaultConfidence (optional) Double Default: 0.4

    Default confidence (score) cutoff. It must be a value between 0.0 and 1.0.

  • defaultEnrichmentPalette (optional) String Default: ColorBrewer Paired colors

    Set the default Brewer palette for enrichment charts. Possible values are the available Brewer palettes: ColorBrewer Set1 colors, ColorBrewer Pastel1 colors, ColorBrewer Set2 colors, ColorBrewer Paired colors, ColorBrewer Dark colors, ColorBrewer Pastel2 colors, ColorBrewer Set3 colors, ColorBrewer Accents, Rainbow OSC, Random, Rainbow.

  • maxProteins (optional) int Default: 100

    Default number of proteins for the disease and PubMed query. It must be a number between 1 and 2000.

  • nTerms (optional) int Default: 5

    Set the default number of terms to use for charts. It must be a number between 1 and 2000.

  • overlapCutoff (optional) Double Default: 0.5

    This is the maximum Jaccard similarity that will be allowed. Values larger than this cutoff will be excluded. It must be a value between 0.0 and 1.0.

  • defaultChannelPalette (optional) String Default: default channel colors

    Set the palette to use for the edge colors of the STRING channels. Possible values are the default default channel colors and the available Brewer palettes: ColorBrewer Set1 colors, ColorBrewer Pastel1 colors, ColorBrewer Set2 colors, ColorBrewer Paired colors, ColorBrewer Dark colors, ColorBrewer Pastel2 colors, ColorBrewer Set3 colors, ColorBrewer Accents, Rainbow OSC, Random, Rainbow.

  • showEnhancedLabels (optional) boolean Default: true

    Shows STRING style labels by default.

  • showGlassBallEffect (optional) boolean Default: true

    Enables STRING glass ball effect by default.

  • showImage (optional) boolean Default: true

    Shows structure images by default.

  • species (optional) String Default: Homo sapiens

    Default species for network queries. It needs to be one of the species in the list available for the STRING database. See also List species.

Example

string settings species="Mus musculus" defaultConfidence=0.7

Sets the default species for network queries to mouse (Mus musculus) and the default confidence cutoff to 0.7.

List of Other commands

List species

string list species

Retrieves the list of all species known to stringApp (all STRING species + viruses from Viruses.STRING), including the taxonomy ID.

Example

string list species

List all STRING core species.

List of Other commands

List selected species

string list selected species

Retrieves a list of selected species known to stringApp, including the taxonomy ID.

Arguments

  • category required String Default: core

    Specify the category of STRING species to list. There are four categories currently (core, periphery, mapped, viral) and one can also choose to list all. Note that the last option is rarely recommended as it takes a long time for the app to output the list.

Example

string list selected species category=core

List all STRING core species.

List of Other commands

Version

string version

Returns the current version of the app.

List of Other commands