Every change Wellknown observed on this MCP server, newest first, with what it was before and what it became. Tool-surface changes carry the definition diff. Nothing here is edited after the fact.
Changed the definition of "string_network_clustering"
⟨26 unchanged words⟩ labels.","examples":[0,1]},"cluster_aware_layout":{"anyOf":[{"enum":[0,1],"type":"integer"},{"type":"null"}],"default":null,"description":"Lay out the network by its clusters, e.g. for a dense network.","examples":[0,1]},"clustering_algorithm":{"anyOf":[{"enum":[" ⟨362 unchanged words⟩ is requested or a broader/narrower threshold is needed."},"show_cluster_names":{"anyOf":[{"enum":[0,1],"type":"integer"},{"type":"null"}],"default":null,"description":"Show cluster names on the image.","examples":[0,1]},"species":{"default":null,"description" ⟨19 unchanged words⟩
Changed the definition of "string_all_interaction_partners", "string_enrichment", "string_enrichment_image_url" and 11 more
⟨36 unchanged words⟩ does TP53 interact with?”** - It differs fromthe `network` tool`string_interactions_query_set`, which only shows interactions **within the input ⟨34 unchanged words⟩
⟨17 unchanged words⟩ string"},"network_flavor":{"anyOf":[{"anyOf":[{"enum":["evidence","confidence","typed"],"type":"string"},{"type":"null"}],"default":null,"description":"Defaults are typed for functional networks, ⟨45 unchanged words⟩ the user requests that edge display style."},{"type":"null"}],"default":null},"
Changed the definition of "string_all_interaction_partners", "string_create_file", "string_enrichment" and 14 more
⟨53 unchanged words⟩ input set** or a limited extension of it.- If the user refers to "physical interactions", "complexes", or "binding", set the network type to "physical".You can filter for strong interactions using `required_score`. ⟨19 unchanged words⟩
{"properties":{"identifiers":{"description":"Required.One or more protein identifiers, separated by carriage return (%0d).Example","examples":["TP53%0dSMO"],"type":"string"},"network_flavor":{"anyOf":[{"anyOf":[{"enum":["evidence","confidence","typed"],"type":"string"},{"type":"null"}],"description":"Defaults are typed for functional networks, evidence for physical networks, and confidence for regulatory networks. Typed returns functional pairs with any physical and directed regulatory attributes that STRING reports; it does not make every pair physical or regulatory. Typed is available only for functional networks. Set evidence or confidence only when the user requests that edge display style."},{"type":"null"}],"default":null},"
Certificate changed, valid to 2026-12-18
Certificate recorded, valid to 2026-10-20
Authorization not required
First tool surface recorded: 17 tools (server version 2.14.7)
Showing the latest 7 events. The API returns up to 500 and filters by kind: ?kind=tool_surface_changed
{"properties":{"expand_category":{"anyOf":[{"anyOf":[{"type":"string"},{"type":"null"}],"default":null,"description":"Return only this enrichment category with ⟨17 unchanged words⟩ ","PMID","NetworkNeighborAL","Keyword"]},{"type":"null"}],"default":null},"proteins":{"description":"One or more protein ⟨7 unchanged words⟩ string"},"species":{"anyOf":[{"anyOf":[{"type":"string"},{"type":"null"}],"default":null,"description":"NCBI/STRING taxon (e.g. 9606 for human, or STRG0AXXXXX). Use only when required."},{"type":"null"}],"default":null}},"required":["proteins"],"type":"object"}
Retrievesthea STRING enrichment figure (image*URL*URL) for a set of proteins.For the enriched terms and FDR values, use `string_enrichment`. - Each figure shows a single enrichment category; call again with another `category` to show a different one. - Use the same proteins and species as the network and enrichment results already shown to the user, so the figure matches them.
{"properties":{"category":{"anyOf":[{"anyOf":[{"enum":["Process","Function","Component", ⟨5 unchanged words⟩ DPO","WPO","ZPO","FYPO","GWAS","Hallmark","Pfam","SMART","InterPro","PMID"," ⟨6 unchanged words⟩ string"},{"type":"null"}],"default":null,"description":"Term category for enrichment. If omitted, ⟨12 unchanged words⟩ for Reactome, and PMID for publications."},{"type":"null"}],"default":null},"color_palette":{"anyOf":[{"anyOf":[{"enum":["mint_blue","red_blue","lime_emerald","green_blue","peach_purple","straw_navy"," ⟨2 unchanged words⟩ string"},{"type":"null"}],"default":null,"description":"Color palette for FDR. If omitted, STRING uses mint_blue."},"graph_type":{"anyOf":[{"enum":["dotplot","barplot"],"type":"string"},{"type":"null"}],"default":null},"group_by_similaritydescription":{"anyOfPlot type: dotplot or barplot (horizontal bar chart). If omitted, STRING uses dotplot."},"group_by_similarity":[{"anyOf":[{"maximum":1,"minimum":0.1,"type":"number"},{"type":"null"}],"default":null,"description":"GroupVisuallysimilargroups terms based onthetermplot.similarity. Default:no0.8.grouping."},{"type"Details:"null"}],"defaultstring_help topic 'enrichment_grouping'.":null},"identifiers":{"description":"Protein identifiers, ⟨6 unchanged words⟩ string"},"number_of_terms_shown":{"anyOf":[{"anyOf":[{"minimum":1,"type":"integer"},{"type":"null"}],"default":null,"description":"Max number of terms shown on plot. Default: 10."},{"typespecies":"null"}],{"default":null},"species":{"anyOf":[{"description":"NCBI/STRING taxon (e.g. 9606 for human, or STRG0AXXXXX).","type":"string"},{"type":"null"}],"default":null},"x_axis":{"anyOf":[{"anyOf":[{"enum":["signal","strength","FDR", ⟨2 unchanged words⟩ string"},{"type":"null"}],"default":null,"description":"X-axisValuevariable/order.shown on the X-axis; also selects and orders the terms. If omitted, STRING uses signal."},{"type":"null"}],"default":null}},"required":["identifiers"],"type":"object"}
{"properties":{"detail_for_term":{"anyOf":[{"anyOf":[{"type":"string"},{"type":"null"}],"default":null,"description":"Exact functional term ID to return ⟨19 unchanged words⟩ shortened, omitted, or replaced with 'many'."},{"type":"null"}],"default":null},"identifiers":{"description":"Separate multiple protein queries ⟨4 unchanged words⟩ ,"type":"string"},"species":{"anyOfdefault":[{null,"description":"NCBI/STRING taxon (e.g. 9606 for human, or STRG0AXXXXX for uploaded genomes).","type":"string"},{"type":"null"}],"default":null}},"required":["identifiers"],"type":"object"}
⟨53 unchanged words⟩ interpretation of enrichment strength and signal (enrichment_scores) - grouping of terms in enrichment figures (enrichment_grouping)
{"properties":{"topic":{"anyOf":[{"anyOf":[{"enum":["gsea","enrichment_scores","enrichment_grouping","large_input","cytoscape","scores","missing_proteins"," ⟨10 unchanged words⟩ string"},{"type":"null"}],"default":null,"description":"Help topic to display. If omitted, returns the available topics."},{"type":"null"}],"default":null}},"type":"object"}
⟨13 unchanged words⟩ ,"type":"string"},"species":{"anyOfdefault":[{null,"description":"NCBI/STRING taxon (e.g. 9606 for ⟨4 unchanged words⟩ uploaded genomes).","type":"string"},{"type":"null"}],"default":null},"species_b":{"anyOf":[{"anyOf":[{"type":"string"},{"type":"null"}],"default":null,"description":"One or more NCBI taxon IDs ⟨9 unchanged words⟩ 4932 for human, fly, and yeast)."},{"type":"null"}],"default":null}},"required":["proteins"],"type":"object"}
⟨20 unchanged words⟩ string"},"network_type":{"anyOf":[{"anyOf":[{"enum":["functional","physical","regulatory"],"type":"string"},{"type":"null"}],"default":null,"description":"Set physical for physical-interaction evidence or ⟨5 unchanged words⟩ Omit for the functional interaction evidence page."},{"typespecies":"null"}],{"default":null},"species":{"anyOf":[{"description":"NCBI/STRING taxon (e.g. 9606 for human, or STRG0AXXXXX for uploaded genomes).","type":"string"},{"type":"null"}],"default":null}},"required":["identifier_a","identifiers_b"] ⟨2 unchanged words⟩
{"properties":{"extend_network":{"anyOf":[{"anyOf":[{"minimum":0,"type":"integer"},{"type":"null"}],"default":null,"description":"Number of additional proteins to add ⟨30 unchanged words⟩ a neighborhood, or show connecting proteins."},{"type":"null"}],"default":null},"network_flavor":{"anyOf":[{"anyOf":[{"enum":["evidence","confidence","typed"],"type":"string"},{"type":"null"}],"default":null,"description":"Defaults are typed for functional networks, ⟨45 unchanged words⟩ the user requests that edge display style."},{"type":"null"}],"default":null},"network_type":{"anyOf":[{"anyOf":[{"enum":["functional","physical","regulatory"],"type":"string"},{"type":"null"}],"default":null,"description":"Omit for the default functional network. ⟨32 unchanged words⟩ regulatory for directed regulatory relationships between proteins."},{"type":"null"}],"default":null},"proteins":{"description":"One or more protein ⟨10 unchanged words⟩ string"},"required_score":{"anyOf":[{"anyOf":[{"maximum":1000,"minimum":0,"type":"integer"},{"type":"null"}],"default":null,"description":"Minimum confidence score for an interaction. ⟨6 unchanged words⟩ requested or a broader/narrower threshold is needed."},{"typespecies":"null"}],{"default":null},"species":{"anyOf":[{"description":"NCBI taxonomy ID (e.g. 9606 for ⟨7 unchanged words⟩ for uploaded genomes).","type":"string"},{"type":"null"}],"default":null}},"required":["proteins"],"type":"object"}
{"properties":{"center_node_labels":{"anyOf":[{"anyOf":[{"enum":[0,1],"type":"integer"},{"type":"null"}],"default":null,"description":"Center protein labels on nodes. Set ⟨6 unchanged words⟩ center labels.","examples":[0,1]},{"type":"null"}],"default":null},"clustering_algorithm":{"anyOf":[{"anyOf":[{"enum":["leiden","MCL","kmeans"],"type":"string"},{"type":"null"}],"default":null,"description":"Leiden identifies natural communities based on ⟨17 unchanged words⟩ proteins into a fixed number of clusters."},{"type":"null"}],"default":null},"clustering_parameter":{"anyOf":[{"anyOf":[{"minimum":0.1,"type":"number"},{"type":"null"}],"default":null,"description":"Controls clustering granularity. For Leiden: resolution ⟨20 unchanged words⟩ of clusters, integer >=2, default 3."},{"type":"null"}],"default":null},"extend_network":{"anyOf":[{"anyOf":[{"minimum":0,"type":"integer"},{"type":"null"}],"default":null,"description":"Add specified number of additional nodes ⟨9 unchanged words⟩ 0, or 10 for single-protein queries."},{"type":"null"}],"default":null},"hide_disconnected_nodes":{"anyOf":[{"anyOf":[{"enum":[0,1],"type":"integer"},{"type":"null"}],"default":null,"description":"Hide unconnected nodes. Set only if ⟨7 unchanged words⟩ unconnected proteins.","examples":[0,1]},{"type":"null"}],"default":null},"inter_cluster_edge_visibility":{"anyOf":[{"anyOf":[{"enum":["faded","dotted","solid", ⟨2 unchanged words⟩ string"},{"type":"null"}],"default":null,"description":"How to display edges between clusters: faded, dotted, solid, or noshow. Defaults to faded."},{"type":"null"}],"default":null},"network_flavor":{"anyOf":[{"anyOf":[{"enum":["evidence","confidence","typed"],"type":"string"},{"type":"null"}],"default":null,"description":"Defaults are typed for functional networks, ⟨45 unchanged words⟩ the user requests that edge display style."},{"type":"null"}],"default":null},"network_type":{"anyOf":[{"anyOf":[{"enum":["functional","physical","regulatory"],"type":"string"},{"type":"null"}],"default":null,"description":"Omit for the default functional network. ⟨32 unchanged words⟩ regulatory for directed regulatory relationships between proteins."},{"type":"null"}],"default":null},"proteins":{"description":"One or more protein ⟨26 unchanged words⟩ string"},"required_score":{"anyOf":[{"anyOf":[{"maximum":1000,"minimum":0,"type":"integer"},{"type":"null"}],"default":null,"description":"Minimum interaction confidence score. Omit for ⟨9 unchanged words⟩ requested or a broader/narrower threshold is needed."},{"typespecies":"null"}],{"default":null},"species":{"anyOf":[{"description":"NCBI/STRING taxonomy ID (e.g. 9606 for human, or STRG0AXXXXX for uploaded genomes).","type":"string"},{"type":"null"}],"default":null}},"required":["proteins"],"type":"object"}
{"properties":{"extend_network":{"anyOf":[{"anyOf":[{"minimum":0,"type":"integer"},{"type":"null"}],"default":null,"description":"Add white nodes to network, based on scores. Default: 0."},{"type":"null"}],"default":null},"hide_disconnected_nodes":{"anyOf":[{"anyOf":[{"enum":[0,1],"type":"integer"},{"type":"null"}],"default":null,"description":"Hide proteins not connected to any ⟨12 unchanged words⟩ unconnected proteins.","examples":[0,1]},{"type":"null"}],"default":null},"network_flavor":{"anyOf":[{"anyOf":[{"enum":["evidence","confidence","typed"],"type":"string"},{"type":"null"}],"default":null,"description":"Defaults are typed for functional networks, ⟨45 unchanged words⟩ the user requests that edge display style."},{"type":"null"}],"default":null},"network_type":{"anyOf":[{"anyOf":[{"enum":["functional","physical","regulatory"],"type":"string"},{"type":"null"}],"default":null,"description":"Omit for the default functional network. ⟨32 unchanged words⟩ regulatory for directed regulatory relationships between proteins."},{"type":"null"}],"default":null},"proteins":{"description":"One or more protein ⟨26 unchanged words⟩ string"},"required_score":{"anyOf":[{"anyOf":[{"maximum":1000,"minimum":0,"type":"integer"},{"type":"null"}],"default":null,"description":"Threshold of significance to include an ⟨12 unchanged words⟩ requested or a broader/narrower threshold is needed."},{"typespecies":"null"}],{"default":null},"species":{"anyOf":[{"description":"NCBI/STRING taxon (e.g. 9606 for human, or STRG0AXXXXX).","type":"string"},{"type":"null"}],"default":null}},"required":["proteins"],"type":"object"}
⟨14 unchanged words⟩ string"},"required_score":{"anyOf":[{"anyOf":[{"maximum":1000,"minimum":0,"type":"integer"},{"type":"null"}],"default":null,"description":"Minimum interaction confidence score. Omit unless a confidence threshold is requested or a broader/narrower threshold is needed."},{"typespecies":"null"}],{"default":null},"species":{"anyOf":[{"description":"NCBI/STRING taxon (e.g. 9606 for human, or STRG0AXXXXX for uploaded genomes).","type":"string"},{"type":"null"}],"default":null}},"required":["identifiers"],"type":"object"}
{"properties":{"detail_for_term":{"anyOf":[{"anyOf":[{"type":"string"},{"type":"null"}],"default":null,"description":"Exact term ID to return as one full protein-name list."},{"type":"null"}],"default":null},"species":{"default":"9606"," ⟨85 unchanged words⟩
⟨23 unchanged words⟩ string"},"show_sequence":{"anyOf":[{"anyOf":[{"enum":["0","1"],"type":"string"},{"type":"null"}],"default":null,"description":"Include sequences. Use only if the user requests sequence data.","examples":["0","1"]},{"typespecies":"null"}],{"default":null},"species":{"anyOf":[{"description":"NCBI taxonomy ID (e.g. 9606 for ⟨7 unchanged words⟩ for uploaded genomes).","type":"string"},{"type":"null"}],"default":null}},"required":["proteins"],"type":"object"}
{"properties":{"center_node_labels":{"anyOf":[{"anyOf":[{"enum":[0,1],"type":"integer"},{"type":"null"}],"default":null,"description":"Center protein names on nodes. Set ⟨6 unchanged words⟩ center labels.","examples":[0,1]},{"type":"null"}],"default":null},"do_not_show_structures":{"anyOf":[{"anyOf":[{"enum":[0,1],"type":"integer"},{"type":"null"}],"default":null,"description":"Remove small protein structure previews from ⟨14 unchanged words⟩ structure previews.","examples":[0,1]},{"type":"null"}],"default":null},"extend_network":{"anyOf":[{"anyOf":[{"minimum":0,"type":"integer"},{"type":"null"}],"default":null,"description":"Add specified number of nodes to ⟨8 unchanged words⟩ , or 10 for single protein queries."},{"type":"null"}],"default":null},"hide_disconnected_nodes":{"anyOf":[{"anyOf":[{"enum":[0,1],"type":"integer"},{"type":"null"}],"default":null,"description":"Hide proteins not connected to any ⟨12 unchanged words⟩ unconnected proteins.","examples":[0,1]},{"type":"null"}],"default":null},"network_flavor":{"anyOf":[{"anyOf":[{"enum":["evidence","confidence","typed"],"type":"string"},{"type":"null"}],"default":null,"description":"Defaults are typed for functional networks, ⟨45 unchanged words⟩ the user requests that edge display style."},{"type":"null"}],"default":null},"network_type":{"anyOf":[{"anyOf":[{"enum":["functional","physical","regulatory"],"type":"string"},{"type":"null"}],"default":null,"description":"Omit for the default functional network. ⟨32 unchanged words⟩ regulatory for directed regulatory relationships between proteins."},{"type":"null"}],"default":null},"proteins":{"description":"One or more protein ⟨26 unchanged words⟩ string"},"required_score":{"anyOf":[{"anyOf":[{"maximum":1000,"minimum":0,"type":"integer"},{"type":"null"}],"default":null,"description":"Threshold of significance to include an ⟨12 unchanged words⟩ requested or a broader/narrower threshold is needed."},{"typespecies":"null"}],{"default":null},"species":{"anyOf":[{"description":"NCBI/STRING taxon (e.g. 9606 for human, or STRG0AXXXXX).","type":"string"},{"type":"null"}],"default":null}},"required":["proteins"],"type":"object"}
{"properties":{"content":{"description":"RequiredSTRING-derived file content. For .tsv/.csv: one rectangular table ⟨34 unchanged words⟩ :"string"},"filename":{"description":"Required.Suggested output filename with a safe extension such ⟨20 unchanged words⟩ a concise name that reflects the STRING analysisresultresult.",for example string-enrichment.tsv."examples":["string-enrichment.tsv"],"type":"string"}},"required":[ ⟨4 unchanged words⟩
⟨273 unchanged words⟩ False Discovery Rate (B-H corrected p-value) - strength: Enrichment effect size, calculated as log10(observed genes / expected genes) - signal: Balanced enrichment-ranking metric combining the observed/expected ratio and -log(FDR) - description: Description of the enriched term Response metadata ⟨55 unchanged words⟩
⟨6 unchanged words⟩ {"type":"null"}],"description":"Optional.Return only this enrichment category with expanded term coverage and a larger per-term gene-list cutoff. Use a category frommetadata.category_summarymetadata.category_summary.",e.g."examples":["Process","KEGG","PMID","NetworkNeighborAL",or Keyword."Keyword"]},{"type":"null"}],"default":null},"proteins":{"description":"Required.One or more protein identifiers, separated by %0d.Example","examples":["SMO%0dTP53"],"type":"string"},"species":{" ⟨4 unchanged words⟩ {"type":"null"}],"description":"Optional.NCBI/STRING taxon (e.g. 9606 for human, or ⟨14 unchanged words⟩
⟨28 unchanged words⟩ {"type":"null"}],"description":"Optional.Term category for enrichment. If omitted, STRING uses ⟨32 unchanged words⟩ {"type":"null"}],"description":"Optional.Color palette for FDR. If omitted, STRING uses ⟨14 unchanged words⟩ {"type":"null"}],"description":"Optional.Group similar terms on the plot. Default: no ⟨3 unchanged words⟩ default":null},"identifiers":{"description":"Required.Protein identifiers, separated by %0d.Example","examples":["SMO%0dTP53"],"type":"string"},"number_of_terms_shown":{" ⟨6 unchanged words⟩ {"type":"null"}],"description":"Optional.Max number of terms shown on plot. Default: ⟨5 unchanged words⟩ "species":{"anyOf":[{"description":"Required.NCBI/STRING taxon (e.g. 9606 for human, or ⟨18 unchanged words⟩ {"type":"null"}],"description":"Optional.X-axis variable/order. If omitted, STRING uses signal."} ⟨8 unchanged words⟩
⟨6 unchanged words⟩ {"type":"null"}],"description":"Optional.Exact functional term ID to return with the ⟨28 unchanged words⟩ "description":"Separate multiple protein queries by %0d.e.g.","examples":["SMO%0dTP53"],"type":"string"},"species":{"anyOf":[{"description":"Required.NCBI/STRING taxon (e.g. 9606 for human, or ⟨15 unchanged words⟩
⟨30 unchanged words⟩ functionality not available via MCP tools (e.g. GSEA,regulatory networks,or large datasets). - meaning ofthenetworklinesedgesinandthetheirnetworkvisual encoding (line_colorsnetwork_edge_legend) - interpretation of enrichment strength and signal (enrichment_scores)
⟨3 unchanged words⟩ "anyOf":[{"enum":["gsea","enrichment_scores","large_input","cytoscape","scores","missing_proteins","missing_species","proteome_annotation","regulatory_networks","how_to_use_string","line_colorsnetwork_edge_legend","version_and_citation","line_colors","enrichment","signal_strength"],"type":"string"},{"type":"null"}],"description":"Optional.Help topic to display. If omitted, returns the ⟨8 unchanged words⟩
{"properties":{"proteins":{"description":"Required.One or more protein identifiers, separated by %0d.Example","examples":["SMO%0dTP53"],"type":"string"},"species":{"anyOf":[{"description":"Required.NCBI/STRING taxon (e.g. 9606 for human, or ⟨16 unchanged words⟩ {"type":"null"}],"description":"Optional.One or more NCBI taxon IDs for target ⟨22 unchanged words⟩
⟨64 unchanged words⟩ the URL is not itself an interaction verdict. The returned page lets the user explore functional, physical, and regulatory relationship views through its tabs. Parameters: - **identifier_a**: Query protein identifier ( ⟨20 unchanged words⟩ e.g. `9606` for human or `10090` for mouse) - **network_type**: Set to `physical` for physical evidence or `regulatory` for directed regulatory evidence. Typical user questions that should trigger this tool ⟨39 unchanged words⟩
{"properties":{"identifier_a":{"description":"Required.Protein A identifier.","type":"string"},"identifiers_b":{"description":"Required.One or more protein B identifiers, separated by %0d.","type":"string"},"speciesnetwork_type":{"anyOf":[{"anyOf":[{"enum":["functional","physical","regulatory"],"type":"string"},{"type":"null"}],"description":"Required.Set physical for physical-interaction evidence or regulatory for directed regulatory evidence. Omit for the functional interaction evidence page."},{"type":"null"}],"default":null},"species":{"anyOf":[{"description":"NCBI/STRING taxon (e.g. 9606 for human, or ⟨16 unchanged words⟩
⟨18 unchanged words⟩ interactions between all proteins in your query set.If user asks for 'physical' or 'complex' use 'physical' network type.- For a **single protein**, the network ⟨21 unchanged words⟩ the network includes all direct interactions between them.- If the user refers to "physical interactions", "complexes", or "binding", set the network type to "physical".- STRING does not store or report information ⟨62 unchanged words⟩
⟨8 unchanged words⟩ {"type":"null"}],"description":"Optional.Number of additional proteins to add to the ⟨35 unchanged words⟩ ":"null"}],"default":null},"network_flavor":{"anyOf":[{"anyOf":[{"enum":["evidence","confidence","typed"],"type":"string"},{"type":"null"}],"description":"Defaults are typed for functional networks, evidence for physical networks, and confidence for regulatory networks. Typed returns functional pairs with any physical and directed regulatory attributes that STRING reports; it does not make every pair physical or regulatory. Typed is available only for functional networks. Set evidence or confidence only when the user requests that edge display style."},{"type":"null"}],"default":null},"network_type":{"anyOf":[{"anyOf":[{"enum":["functional","physical","regulatory"],"type":"string"},{"type":"null"}],"description":"Optional.Omit forSTRINGthe default functionalassociations.network.SetIts typed view can include physicalonlyand directed regulatory attributes when STRING returns them; inspect `physical` and `regulatory.directions` before claiming those edge types. Set physical for binding, complex, or co-complex questions. Set regulatory for directed regulatory relationships between proteins."},{"type":"null"}],"default":null},"proteins":{"description":"Required.One or more protein identifiers, separated by carriage return (%0d).Example","examples":["SMO%0dTP53"],"type":"string"},"required_score":{" ⟨8 unchanged words⟩ {"type":"null"}],"description":"Optional.Minimum confidence score for an interaction. Omit unless ⟨15 unchanged words⟩ "species":{"anyOf":[{"description":"Optional.NCBI taxonomy ID (e.g. 9606 for human) ⟨20 unchanged words⟩
Performs **network clustering** on a STRING interaction network and returnsbotha**networknetwork imageURL**URL, an interactive STRING network URL, and details about each detected cluster. Provide a table with each detected cluster’s color, STRING-derived functional description, and any returned features that distinguish it from the others. Use the same parameters as in the network ⟨15 unchanged words⟩ of clusters may differ from the requested value.DashedInter-clusterlinesedgesrepresentareconnectionsfadedbetweenbyclusters,default.whileUsesolid`inter_cluster_edge_visibility`linestoindicateselectinteractionsawithindifferentclusters.display style. Notes: - For small queries (≤5 proteins ⟨14 unchanged words⟩ is produced, try increasing `required_score`, adjusting theinflationclustering parameter, or switching to`kmeans`a physical network forsmall,ahighlysparserinterconnectedinteractionnetworks.map.
⟨9 unchanged words⟩ {"type":"null"}],"description":"Optional.Center protein labels onnodes when set to 1.nodes. Set only if the user asks to center labels.","examples":[0,1]},{"type":"null"}],"default" ⟨3 unchanged words⟩ ":[{"anyOf":[{"enum":["leiden","MCL","kmeans"],"type":"string"},{"type":"null"}],"description":"Optional.Leiden identifies natural communities based on network connectivity and is the default. MCL identifies densely connected subnetworks based on connectivity flow. kmeans partitions proteins into a fixed number of clusters.If omitted, the server uses MCL."},{"type":"null"}],"default ⟨2 unchanged words⟩ "anyOf":[{"anyOf":[{"minimum":10.1,"type":"number"},{"type":"null"}],"description":"Optional.Controls clustering granularity. ForMCLLeiden:inflationresolution parameter1.0-10.00.1-10.0, default3.0;1.0;
⟨33 unchanged words⟩ includes all known interactions **within the query set**.- If the user asks for "physical interactions", "complexes", or "binding", set `network_type` to "physical".The input may include one numeric value per ⟨125 unchanged words⟩
⟨8 unchanged words⟩ {"type":"null"}],"description":"Optional.Add white nodes to network, based on scores. ⟨14 unchanged words⟩ {"type":"null"}],"description":"Optional.Hide proteins not connected to any otherprotein when set to 1.protein. Set only if the user asks to hide disconnected or unconnected proteins.","examples":[0,1]},{"type":"null"}],"default" ⟨4 unchanged words⟩ ":[{"enum":["evidence","confidence","typed"],"type":"string"},{"type":"null"}],"description":"Optional.DefaultsEdgearestyle.typedOmitfor functional networks, evidence for physical networks, and confidence for regulatory networks. Typed returns functional pairs with any physical and directed regulatory attributes that STRINGdefaultreports;evidenceitstyling.doesSetnotonlymakewheneverythepairuserphysicalasksor regulatory. Typed is available only for functional networks. Set evidence or confidence only when the user requests that edgedisplay.display style."},{"type":"null"}],"default ⟨4 unchanged words⟩ ":[{"enum":["functional","physical","regulatory"],"type":"string"},{"type":"null"}],"description":"Optional.Omit forSTRINGthe default functionalassociations.network.SetIts typed view can include physicalonlyand directed regulatory attributes when STRING returns them; inspect `physical` and `regulatory.directions` before claiming those edge types. Set physical for binding, complex, or co-complex questions. Set regulatory for directed regulatory relationships between proteins."},{"type":"null"}],"default":null},"proteins":{"description":"Required.One or more protein IDs, optionally followed by one numeric value per protein.Example:\nPTEN 0.234\nSMO -3.445\nUseUse newline (%0d) between entries. Tabs and spaces are accepted as separators.","examples":["PTEN 0.234\nSMO -3.445"],"type":"string"},"required_score":{"anyOf" ⟨7 unchanged words⟩ {"type":"null"}],"description":"Optional.Threshold of significance to include an interaction. Omit ⟨21 unchanged words⟩ "species":{"anyOf":[{"description":"Required.NCBI/STRING taxon (e.g. 9606 for human, or ⟨12 unchanged words⟩
{"properties":{"identifiers":{"description":"Required.One or more protein identifiers, separated by %0d.Example","examples":["SMO%0dTP53"],"type":"string"},"required_score":{" ⟨8 unchanged words⟩ {"type":"null"}],"description":"Optional.Minimum interaction confidence score. Omit unless a confidence ⟨13 unchanged words⟩ "species":{"anyOf":[{"description":"Required.NCBI/STRING taxon (e.g. 9606 for human, or ⟨15 unchanged words⟩
⟨6 unchanged words⟩ {"type":"null"}],"description":"Optional.Exact term ID to return as one full ⟨66 unchanged words⟩ :"string"},"term_text":{"description":"Required.Functional term identifier (GO, KEGG, Reactome, etc.) or descriptive freetext (e.g. 'hsa05218'text.",'Melanoma'"examples":["hsa05218",'GO"Melanoma","GO:0008543'0008543",'Fibroblast"Fibroblast growthfactor').factor"],"type":"string"}},"required":[ ⟨3 unchanged words⟩
{"properties":{"species_text":{"description":"Required.One species/clade search term or multiple NCBI taxon IDs separated by carriage return (%0d).Examples: 'human', 'mouse', 'vertebrates', '511145', or '9598%0d10090'.For multiple queries, use taxon IDs rather than free-text names.","examples":["human","mouse","vertebrates","511145","9598%0d10090"],"type":"string"}},"required":[ ⟨3 unchanged words⟩
{"properties":{"proteins":{"description":"Required.One or more input protein identifiers (gene symbols, UniProt IDs, etc.), separated by carriage return (%0d).Example","examples":["TP53%0dSMO"],"type":"string"},"show_sequence":{" ⟨7 unchanged words⟩ {"type":"null"}],"description":"Optional.Includesequences when set to 1.sequences. Use only if the user requests sequence data.","examples":["0","1"]},{"type":"null"}],"default":null},"species":{"anyOf":[{"description":"Optional.NCBI taxonomy ID (e.g. 9606 for human) ⟨20 unchanged words⟩
⟨38 unchanged words⟩ "species":{"default":9606,"description":"Required.NCBI or STRING taxonomy ID. You can query ⟨22 unchanged words⟩
⟨33 unchanged words⟩ includes all known interactions **within the query set**.- If the user asks for "physical interactions", "complexes", or "binding", set `network_type` to "physical".The input may include one numeric value per ⟨129 unchanged words⟩
⟨9 unchanged words⟩ {"type":"null"}],"description":"Optional.Center protein names onnodes when set to 1.nodes. Set only if the user asks to center labels.","examples":[0,1]},{"type":"null"}],"default" ⟨9 unchanged words⟩ {"type":"null"}],"description":"Optional.Remove small protein structure previews from inside the nodebubbles when set to 1.bubbles. Set only if the user asks to remove or hide structure previews.","examples":[0,1]},{"type":"null"}],"default" ⟨8 unchanged words⟩ {"type":"null"}],"description":"Optional.Add specified number of nodes to the network, ⟨24 unchanged words⟩ {"type":"null"}],"description":"Optional.Hide proteins not connected to any otherprotein when set to 1.protein. Set only if the user asks to hide disconnected or unconnected proteins.","examples":[0,1]},{"type":"null"}],"default" ⟨4 unchanged words⟩ ":[{"enum":["evidence","confidence","typed"],"type":"string"},{"type":"null"}],"description":"Optional.DefaultsEdgearestyle.typedOmitfor functional networks, evidence for physical networks, and confidence for regulatory networks. Typed returns functional pairs with any physical and directed regulatory attributes that STRINGdefaultreports;evidenceitstyling.doesSetnotonlymakewheneverythepairuserphysicalasksor regulatory. Typed is available only for functional networks. Set evidence or confidence only when the user requests that edgedisplay.display style."},{"type":"null"}],"default ⟨4 unchanged words⟩ ":[{"enum":["functional","physical","regulatory"],"type":"string"},{"type":"null"}],"description":"Optional.Omit forSTRINGthe default functionalassociations.network.SetIts typed view can include physicalonlyand directed regulatory attributes when STRING returns them; inspect `physical` and `regulatory.directions` before claiming those edge types. Set physical for binding, complex, or co-complex questions. Set regulatory for directed regulatory relationships between proteins."},{"type":"null"}],"default":null},"proteins":{"description":"Required.One or more protein IDs, optionally followed by one numeric value per protein.Example:\nPTEN 0.234\nSMO -3.445\nUseUse newline (%0d) between entries. Tabs and spaces are accepted as separators.","examples":["PTEN 0.234\nSMO -3.445"],"type":"string"},"required_score":{"anyOf" ⟨7 unchanged words⟩ {"type":"null"}],"description":"Optional.Threshold of significance to include an interaction. Omit ⟨21 unchanged words⟩ "species":{"anyOf":[{"description":"Required.NCBI/STRING taxon (e.g. 9606 for human, or ⟨12 unchanged words⟩