Schemas

There are four schemas in STRING that describes different aspects of the content.

schema	description
evidence	contains info of the underlying evidence for interactions.
homology	blast hits used to propagate evidence to other species by means of homology.
items	info about entries (protein names, species, orthgroups, etc.).
network	the interactions and their scores.

Table: evidence.abstracts

Abstracts are used for showing the text bodies in the text-mining view.

field	description
abstract_id	abstract identifier (e.g. "PMID019234442", "OMIM000100070", etc.).
publication_date	date of publication (e.g. "2009").
publication_source	source. the name of journal(e.g. "Nature").
linkout_url	link to publication.
title	title of publication.
body	the abstract of the publication.

Table: evidence.collections

The different sources of data from where STRING imports data (for the channels 'experiments' and 'databases').

field	description
collection_id	the name of the data source (e.g. "dip").
pubmed_id	the pubmed identification number (e.g. "14681454").
comment	short description of the data and the date it was imported.

Table: evidence.evidence_transfers

Evidence of interaction propagated across species using homology.

field	description
target_protein_id_a	interactor A that have received evidence from source.
target_protein_id_b	interactor B that have received evidence from source.
transfer_score_c1	fraction of transfer score for interactor A. depends on how ambiguous the homology is. range from 0 to 1, higher score is better.
transfer_score_c2	fraction of transfer score for interactor A.
source_ascore	coexpression score of the source interaction.
source_escore	experimental score of the source interaction.
source_dscore	database score of the source interaction.
source_tscore	textmining score of the source interaction.

Table: evidence.fusion_evidence

Homology propagated evidence for fusion evidence, which originates from only one source protein.

field	description
target_protein_id_a	interactor A that have received evidence from source.
target_protein_id_b	interactor A that have received evidence from source.
source_protein	the source from which evidence for the interaction have have been transferred.
source_species	species_id for the species of the source of the evidence.
transfer_score_c1	homology fraction of score.
transfer_score_c2	homology fraction of score.
fusion_score	fusion score of the source interaction.

Table: evidence.items_abstracts

The abstracts in which a protein is mentioned.

field	description
protein_id	internal protein identifier.
abstract_id	abstract identifier.
name	name of gene in abstract.
abstract_length	length of abstract in number of characters.
mesh_id	identifier for MeSH (i.e. the controlled vocabulary of NCBI for different names that refer to the same concept).

Table: evidence.orthgroups_abstracts

The abstracts that mention any member of a orthologous group (redundant table w.r.t. evidence.items_abstracts)

field	description
orthgroup_id	internal orthologs group identifier.
abstract_id	abstract identifier.

Table: evidence.orthgroups_sets

The sets that support evidence for interaction between orthologs groups.

field	description
orthgroup_id	internal orthologs group identifier.
set_id	the identifier to external repository from where evidence was gathered
is_database_set	this flag is set to 'true' when the set concerns the 'database' channel in STRING (as opposed to the 'experiments' channel)

Table: evidence.sets

The sets of evidence that support interactions.

field	description
set_id	the identifier to external repository from where evidence was gathered (e.g. "BCRT1314").
collection_id	the external repository (e.g. "biocarta").
title	type of evidence (e.g. "curated pathway").
comment	auxiliary information of the set.
url	link to original data.

Table: evidence.sets_items

The members in the evidence sets. An interaction exists if two lines have the same set_id. set_id | identifier to a single of proteins in an external repository (protein complex, pathway or binary pair).

field	description
protein_id	internal protein identifier.
species_id	taxonomy identifier.
is_database_set	this flag is set to 'true' when the set concerns the 'database' channel in STRING (as opposed to the 'experiments' channel).

Table: evidence.sets_pubmedrefs

Supporting papers from external repository.

field	description
set_id	identifier to external repository.
pubmed_id	pubmed identifier.

Table: homology.best_hit_per_species

Derived homology information that is used for transfer of evidence.

field	description
protein_id	internal protein identifier.
species_id	taxonomy identifier of the species to which the alignment is found.
nr_high_scoring_hits	number of proteins in the species that have blast bit scores higher than 60.
best_hit_protein_id	the id of the protein with the highest scoring alignment.
best_hit_identifier	the string preferred name of the highest scoring alignment.
best_hit_bitscore	the bitscore of the highest scoring alignment.
best_hit_normscore	score normalized by the self-hit of the longer protein.
best_hit_alignment_length	the length of the alignment.

Table: homology.blast_data

Raw data of all-against-all BLAST alignments.

field	description
protein_id_a	internal identifier of protein A.
protein_id_b	internal identifier of protein B.
bitscore	bitscore of alignment (higher is better).
start_a	amino acid where alignment start.
end_a	amino acid where alignment stop (c.f. length_of_alignment_a = end_a
start_b	amino acid where alignment start.
end_b	amino acid where alignment stop.
size_b	length of protein B.

Table: items.funccats

The functional categories defined by the COG database.

field	description
funccat_id	one-letter identifier of functional category.
funccat_description	description of function (e.g. "Transcription").

Table: items.genes

Information of the genes that are used for neighborhood evidence.

field	description
gene_id	internal gene identifier.
gene_external_id	external gene identifier (e.g.: "257311.BPP1623.NC_002928.1731802")
start_position_on_contig	the nucleotide of the start of the ORF.
end_position_on_contig	the nucleotide where the ORF ends.
protein_size	size of the protein (usually the longest splice variant).

Table: items.genes_proteins

Mapping between the internal identifier of genes and proteins.

field	description
protein_id	internal protein identifier.
gene_id	internal gene identifier.

Table: items.meshterms

Mesh (Medical Subject Headings) describe a controlled vocabulary when names and categories can not be distinguished.

field	description
mesh_id	MeSH identifier (e.g. 2826)
description	Description of MeSH term (e.g."Chorismate Mutase")

Table: items.orthgroups

Information of orthologous groups.

field	description
orthgroup_id	internal orthologs groups identifier.
orthgroup_external_id	name of orthologs group (e.g. "COG0133").
description	general description of biological functionality.
protein_count	number of members in orthologs group.
species_count	number of distinct species in group.

Table: items.orthgroups_funccats

The functional category of a orthologs group.

field	description
orthgroup_id	internal orthologs groups identifier.
funccat_id	one-letter identifier of functional category.

Table: items.orthgroups_species

This describes how many genes in a given organism encode a gene from a given orthologous group.

field	description
orthgroup_id	internal orthologs groups identifier.
species_id	taxonomy identifier.
count	number of genes.

Table: items.protein_image_match

Information about protein structure images used for the nodes in the network view.

field	description
protein_id	internal protein identifier.
image_id	internal identifier of an protein structure image.
identity	the percentage identity to the most similar protein.
source	the origin of the protein structure.
start_position_on_protein	from which position of the protein a structure is mapped.
end_position_on_protein	to which position of the protein a stucture is mapped.
annotation	the name of the structure.

Table: items.proteins

Information about the proteins in STRING.

field	description
protein_id	internal protein identifier.
protein_external_id	taxonomy identifier and name of protein concatenated.
species_id	taxonomy identifier.
protein_checksum	checksum of the protein sequence.
protein_size	length of the protein (in amino acids).
annotation	description of the functionality of protein.
preferred_name	the preferred name of STRING (e.g. "amiF")
annotation_word_vectors	internal use only: enables full-text searching.

Table: items.proteins_meshterms

Mapping between MeSH and STRING.

field	description
mesh_id	MeSH id.
protein_id	internal protein identifier.

Table: items.proteins_names

Mapping of various names to string entries

field	description
protein_name	a name of the protein (e.g. "amiF", "spr1703", "AE008535", etc.)
protein_id	internal protein identifier.
species_id	taxonomy identifier.
source	the origin of the name (e.g. "Ensembl")
is_preferred_name	"true" if the name is the preferred string name.

Table: items.proteins_orthgroups

Description of the members in the orthologs groups.

field	description
protein_id	internal protein identifier.
orthgroup_id	to which orthgroup the protein belongs (internal orthgroup id).
species_id	taxonomy identifier of the protein.
start_position	residue within the protein where the orthologous group mapping starts.
end_position	residue within the protein where the orthologous group mapping ends.
preferred_name	preferred name of protein (redundant w.r.t items.proteins_names).
protein_annotation	annotated function of protein (redundant w.r.t items.proteins_names).

Table: items.proteins_sequences

Describes the sequence of the protein.

field	description
protein_id	internal protein identifier.
sequence	protein sequence.

Table: items.proteins_smartlinkouts

Links to the SMART database describing the domain structures of a protein.

field	description
protein_id	internal protein identifier.
protein_size	length of protein in amino acids.
smart_url	link to SMART database entry.

Table: items.runs"

Neighborhood evidence: this describes an un-interrupted group of neighboring genes a ('run').

field	description
run_id	internal id.
species_id	taxonomy identifier.
contig_id	from genome assembly information: which chromosome or otherwise identified contig the run is on.

Table: items.runs_genes_proteins

Mapping of between runs, genes and proteins.

field	description
run_id	internal id.
gene_id	internal gene identifier.
protein_id	internal protein identifier.
start_position_on_contig	the nucleotide of the start of the ORF.
end_position_on_contig	the nucleotide where the ORF ends.
preferred_name	the preferred name of STRING.
annotation	functional annotation of protein.

Table: items.runs_orthgroups

Describes which orthologous groups map to an un-interrupted group of genes on the chromosome.

field	description
run_id	internal id.
orthgroup_id	internal orthologs groups identifier.

Table: items.species

Information on the organisms in STRING.

field	description
species_id	taxonomy identifier (e.g "9606" for human).
official_name	scientific name of organism.
compact_name	other name, shortened version of the scientific name.
kingdom	to which of the 3 different highest grouping in the taxonomy the organism belong.
type	If the organism is a core species or periphery species. Core species are BLAST aligned all-against-all, periphery only against the core.

Table: items.species_names

NCBI taxonomy used for organism selection on input page.

field	description
species_id	taxonomy identifier .
species_name	species synonym.
official_name	scientific name of organism.

Table: items.species_nodes

Auxiliary table to NCBI organism selection (c.f. items.species_names).

field	description
species_id	taxonomy identifier.
species_name	name of query.
position	position of fist clade member in a STRING clade.
size	number of string species in the NCBI clade.

Table: network.actions

The type of an interaction

field	description
item_id_a	internal protein identifier.
item_id_b	internal protein identifier.
mode	type of interaction ("reaction", "expression", "activation", "ptmod"(post-translational modifications), "binding", "catalysis")
action	the effect of the action ("inhibition", "activation")
a_is_acting	the directionality of the action if applicable (1 gives that item_id_a is acting upon item_id_b)
score	the best combined score of all interactions in string.

Table: network.best_combined_scores_orthgroups

Derived table of best combined score between two orthologs groups.

field	description
orthgroup_id	internal orthologs group identifier.
best_score	the highest score of any members between two orthologs group.

Table: network.best_combined_scores_proteins

The highest interaction scores of a protein.

field	description
protein_id	internal protein identifier.
best_score	the best combined score of all interactions in string.

Table: network.node_node_links

The interactions and their scores between proteins in a species (and orthologs groups)

field	description
node_id_a	internal identifier (equivalent to protein_id).
node_id_b	internal identifier (equivalent to protein_id).
node_id_b	taxonomy identifier (equivalent to species_id).
combined_score	the combined score of all the evidence scores (including transferred scores).
evidence_score	the scores of the individual channels represented as a list of score types and their score. For example, {{4,626}} means that coocurrance score (4) is 0.626. The types of score can be found in table network.score_types.

The combined_score is multiplied by 1000 to represent a score that range from 0 to 1 (as an integer from 0 to 1000).

Table: network.score_types

field	description
score_id	internal identifier
score_type	the type of the score, see below

score_type	name	description
1	equiv_nscore	neighborhood score, (computed from the inter-gene nucleotide count).
2	equiv_nscore_transferred	neighborhood score from other species (via homology).
3	equiv_fscore	fusion score (derived from fused proteins in other species).
4	equiv_pscore	cooccurence score of the phyletic profile (derived from similar absence/presence patterns of genes).
5	equiv_hscore	homology score, the degree of homology of the interactors (trivial and normally not reported in STRING).
6	array_score	coexpression score (derived from similar patter of mRNA expression measured by DNA arrays and similar technologies).
7	array_score_transferred	coexpression score transferred by homology from other species.
8	experimental_score	experimental score (derived from experimental data, such as, affinity chromatography).
9	experimental_score_transferred	experimental score transferred by homology from other species.
10	database_score	database score (derived from curated data of various databases).
11	database_score_transferred	database score transferred by homology from other species.
12	textmining_score	textmining score (derived from co-occurring mentioning of gene/protein names in abstracts).
13	textmining_score_transferred	textmining score transferred by homology from other species.
14	neighborhood_score	raw neighborhood counts for COG mode (deprecated).
15	fusion_score	raw fusion score for COG mode (deprecated).
16	cooccurence_score	raw cooccurence score for COG mode (deprecated).