biologists and bioinformaticians have made extensive use of protein interaction information to interpret experimental results in the context of a global protein interaction network and to test new hypotheses .
protein interaction databases have played a major role in capturing this information from the literature and in presenting it in a structured format to interested users .
nevertheless no single database covers the entire interaction information reported in the literature and , to achieve the largest possible coverage , users or online resources are forced to combine data downloaded from different databases with different data models and ontologies ( 14 ) . to facilitate the exchange and integration of molecular interactions by data providers , databases and data users , the molecular interaction group of the human proteome organization 
protein standard initiative , has proposed a data representation standard ( current version psi - mi 2.5 ) ( 5 ) .
this standard has been adopted by the major protein  protein interaction ( ppi ) databases and has formed the basis for the emergence of the international molecular exchange ( imex ) consortium ( http://imex.sourceforge.net/ ) ( 6 ) .
imex follows the model of similar initiatives in different domains of biological data , such as the nucleotide sequence exchange between embl ( 7 ) , genbank ( 8) and ddbj ( 9 ) , and aims at distributing the curation workload between participating databases thus avoiding work duplication and increasing literature coverage .
the databases adhering to this consortium have developed and adopted a common curation manual ( http://imex.sourceforge.net/doc/imex-curationmanual.doc ) , describing both the information that should be captured by the member databases and how the information should be represented .
the consortium currently comprises four active members : dip ( 10 ) , intact ( 11 ) , matrixdb ( 12 ) and mint ( 13 ) .
the psi - mi controlled vocabulary , a major component of the psi - mi and imex data representation standard , defines interactions in a broad sense .
two proteins are said to interact if they score positive in any of the many experimental procedures used to detect molecular interactions , without implying that they make direct physical contact .
however , the experimental evidence is clearly defined in associated database records leaving users free to assess confidence for a given piece of experimental evidence . that is , each entry is annotated with the supporting methods , some of which are understood to provide evidence of direct physical contact between the partner proteins such as x - ray crystallography , nuclear magnetic resonance , biochemical assays carried out on purified proteins , and those for which the presence of bridging molecules can not be excluded such as , pull - down , co - immunoprecipitation and two hybrid assays . a recent major advance in the protein interaction field
is the community definition of the minimal information required for reporting a molecular interaction experiment ( mimix ) ( 14 ) .
authors reporting protein interaction information in their manuscripts are asked to follow this guidelines , ensuring that this 
minimal information is unambiguously described with controlled vocabularies and cross - references to major public databases .
the checklist contains information such as the name and organism of the proteins , their experimental role ( bait , prey ) , or the detection method .
mint , as a member of the imex consortium , is one of the major ppi repositories .
the database content has grown ( more than 19 000 experimental evidences have been added since the last report in 2006 ) , the curation policy has been updated to meet psi standards , and the web interface has become more user friendly with the development of new query and graphic tools . in addition each interaction is now annotated with a score ranging from 0 to 1 reflecting the quality and quantity of experimental information supporting the interaction .
over the past three years in concert with other databases , mainly intact and dip , the annotation policy has been reviewed to meet the standards of psi - mi and the guidelines of the imex consortium .
one major advance of the psi - mi standard has been the replacement of the  physical interaction term with two new definitions that permit to discriminate between interactions that have a clear experimental evidence for direct contact between the two partners ( physical association ) and those where the direct contact is not demonstrated ( association ) .
each article is curated in its entirety , following the psi - mi recommendations , and all the interactions and the experimental details of their supporting evidences are captured in the database entries .
there has recently been some vociferous debate between some data providers and databases regarding the role of database curators with respect to assessment of data quality or reliability ( 15 ) ( thorneycroft et al .
to clarify , the mint curation process does not involve any judgment of the accuracy of the published evidence and curators do not make any assessment or ad - hoc reliability ranking of the different interactions reported in a peer reviewed article .
this supporting evidence can then be used by database users to filter the data according to their own reliability standards . in order to facilitate the navigation of the results of a query , the mint database associate to each interaction a reliability score ( described below ) that takes into account the experimental support .
mint relies on the work of two professional curators and , as a member of the imex consortium , has been assigned the task of curating four journals : febs letters , embo journal , embo reports and more recently the febs journal .
all ppi described in an article published by one of these journals are added to mint according to the imex manual .
furthermore , as many high - throughput datasets are published by journals not covered by the imex consortium , these articles are curated in rotation by the three member databases .
whereas most entries are curated after publication , mint has begun collaborating with febs letter and febs journal on an editorial procedure that , as recommended by the mimix guidelines , involves pre - publication participation of the manuscript authors in the curation process ( 16 ) .
the journal editorial offices submit accepted articles to mint curators who , in concert with authors , process the protein interaction information as database entries .
the processed information is returned to the journal publisher as a structured digital abstract ( sda ) , where all the interactions described in the article are summarized in a short structured sentence that uses a controlled vocabulary and is appended at the end of the traditional abstract .
this sda can be easily parsed by automatic software and , in the online version of the manuscript , they are hyperlinked to relevant databases .
as a consequence of limited support ( i.e. small curation team ) and of the curation depth required by imex , mint does not cover all the protein interactions reported in the literature . to increase the coverage in domains of particular interest to our experimental group
, mint also contains entries that are not fully imex compliant , albeit adhering to the psi - mi model and controlled vocabularies .
light curation and has allowed an increase in the number of articles curated per time unit
. for example mint has a very high coverage of the experimental evidence supporting interactions mediated by modular domains such as sh3 , sh2 or 14 - 3 - 3 domains , similarly most interactions between viral and host proteins are annotated in mint .
many of the articles supporting these interactions were curated to a lower level of detail than recommended by imex , and only the information required by the mimix guidelines were captured by curators .
the differences between imex curation and light ( mimix based ) curation is summarized in table 1 . 

table 1.differences between imex and light curationannotationimex curationlight curationadditional information / examplespublicationreferencepmid / d.o.i.interactionfigurefigure , tableinteractioninteraction typedirect , physical , enzymatic reactionexperimentdetection methodco - immunoprecipitation , two - hybridexperimentbiosourcetaxid , cell type , tissueinteractorauthor given nameinteractorcross referenceuniprotkb , refseqinteractororganismtaxidinteractorexperimental rolebait / preyinteractorbiological roleenzyme , enzyme target western blotinteractorparticipant identificationinteractorexpression levelendogenous / over - expressed purificationinteractorsample processinteractortaginteractorbinding siterange , domaininteractormodificationphosphorylation , resulting / required position , amino - acidsinteractormutation differences between imex and light curation it is important to understand that entries curated according to the light curation model are as accurate as the imex ones .
the same controlled vocabularies , proposed by the psi - mi consortium , are used and in both cases , for instance , the annotator makes a distinction between direct interactions and physical associations , where the experimental evidence can not prove direct association between the partners .
most of these light curation entries are annotated by experimentalists that are specialists in the given biological domain and are reviewed by one of the professional curators .
the differences between the two curation models do not affect most users , mainly looking for high quality data , but should be taken into consideration when the analysis requires more details about the experimental setup .
the entries that are not annotated according to the imex manual are clearly labeled in the web - interface and in the exported files .
in addition , a  light curator may choose to capture from an article only those interactions related to his topic of interest , for instance interactions involving a specific domain , and skip additional interaction information that may be present in the same article .
this label may be used by users that only want to focus on imex data , and by curators who may later complete those entries . in 2009 the oldest interactions in mint , for which these policies had not been followed , have been blocked and hidden to the users .
once an interaction is curated and validated in mint it is automatically imported , according to its properties , by one or more sister databases .
homomint ( http://mint.bio.uniroma2.it/homomint ) ( 17 ) is a database of human interactions that are either experimentally verified or inferred from model organisms .
each time an interaction between human proteins is deposited into mint , it is automatically imported into homomint .
the interactions between proteins of model organisms ( for instance rat , mouse , yeast , worm or fly ) are imported into homomint after mapping to the human orthologs .
orthologs are retrieved from ensembl compara through the biomart webservice ( http://www.ensembl.org/biomart/martview ) ( 18 ) .
the information about the species in which the interaction was experimentally demonstrated is maintained in the homomint entry .
the database of domain  peptide interactions , domino ( http://mint.bio.uniroma2.it/domino ) ( 19 ) , focuses on interactions mediated by domains ( sh3 , sh2 , 14 - 3 - 3 , pdz , etc . ) . wherever the domain mediating an interaction is specified in the mint entry , the entry is automatically imported into domino .
in addition domino contains interactions between domains and peptides that are not present in proteins ( for instance peptides selected by phage display ) and offers a different interface , including the domino viewer applet in which the modular composition of the proteins is displayed .
finally , all virus  virus and virus  host interactions in mint are automatically transferred to virusmint ( http://mint.bio.uniroma2.it/virusmint ) ( 20 ) .
virusmint has a specialized interface which focuses on virus interactomes , completed with host interactions connecting the viral networks .
this is partly due to experimental false positives , especially in high throughput experiments and partly to the different sensitivity and specificity of the diverse experimental setups .
thus , as it remains difficult for the final user to assess the quality of each binary interaction , we have developed a scoring system to facilitate the evaluation of the reliability of each single interaction , with particular focus on direct physical interactions ( 21 ) .
the mint scoring system reflects the quantity and quality of independent supporting evidence stored in the database .
cumulative evidence as the sum of all the supporting evidence weighted by coefficients that reflects the confidence in the specific approach .
this is based on : 
  the size of the experiment : experiments are defined large scale if the article reporting them describes more than 50 interactions , otherwise they are defined small scale . as only the 0.01% of the stored articles report more than 50 interactions we considered this a reasonable threshold to distinguish between large and small scale experiments. the type of experiment supporting the interaction. it emphasizes evidence of direct interaction ( i.e. two - hybrid ) with respect to experimental support that does not provide unequivocal evidence of direct interaction ( i.e. in vivo co - immunoprecipitation). the number of interaction partners detected in a single purification. the sequence similarity of ortholog proteins , for interactions mapped to the human proteome in homomint. the number of different publications supporting the interaction . 

the resulting score ranges between 0 and 1 and only well supported interactions obtain a value close to 1 .
more details and updates about the score are available at http://mint.bio.uniroma2.it/mint/doc/mint-confidence-score.html .  the size of the experiment : experiments are defined large scale if the article reporting them describes more than 50 interactions , otherwise they are defined small scale . as only the 0.01% of the stored articles report more than 50 interactions we considered this a reasonable threshold to distinguish between large and small scale experiments .  the type of experiment supporting the interaction .
 it emphasizes evidence of direct interaction ( i.e. two - hybrid ) with respect to experimental support that does not provide unequivocal evidence of direct interaction ( i.e. in vivo co - immunoprecipitation ) . 
the number of interaction partners detected in a single purification .  the sequence similarity of ortholog proteins , for interactions mapped to the human proteome in homomint .  the number of different publications supporting the interaction .
the scoring system , as illustrated in figure 1 , is an effective tool for filtering interactions . in panel ( a ) we have displayed all the proteins that , according to the mint database interact with the proteins participating in the egfr pathway as defined by the reactome database ( 22 ) .
panel ( b ) shows the network that is obtained after removing interactions that are below a certain confidence threshold .
interestingly , the remaining interactions can be easily recognized by any biologist familiar with this pathway ( e.g. efgr - grb2 , efgr - shc1 ) . 

the network in panel ( b ) is obtained by removing interactions below a certain confidence threshold ( 0.72 ) .
the network in panel ( b ) is obtained by removing interactions below a certain confidence threshold ( 0.72 ) .
mint can be queried online using the web interface available at http://mint.bio.uniroma2.it / mint/. the list of molecules that have been shown to interact with a chosen query protein may be displayed either as text on an html page or as a graph in the viewer applet . in the html output page ( figure 2 ) ,
we have recently added new columns to provide an overview of the type of evidence supporting the interaction .
we distinguish between experimental evidence for direct interactions , associations ( we group here both psi - mi terms association and physical association ) , enzymatic reactions and co - localizations .
the number of experiments supporting the association of the two proteins in a larger complex and the number of high throughput experiments are indicated in the last two columns . 

proteins partners of the e3 ubiquitin - protein ligase cbl . in the right frame interactors
the total number of evidences is provided as well as the number of direct interactions , physical associations ( the two psi - mi terms physical association and association are grouped here ) , colocalizations and enzymatic reactions . even if enzymatic reactions are considered according to psi - mi standard as a subtype of direct interactions ,
there are counted here only as enzymatic reaction . the number of evidences by high throughput experiment and the number of evidences in which the two proteins are part of a larger complex are indicated in the last two columns .
each figure in the different columns is linked to the description of the evidences supporting the interaction . by clicking the 
22 link on the first row one obtains the information in the the left frame where the evidences for sh3kbp1 as a partner of cbl are grouped by publication and detection method .  
proteins partners of the e3 ubiquitin - protein ligase cbl . in the right frame interactors
the total number of evidences is provided as well as the number of direct interactions , physical associations ( the two psi - mi terms physical association and association are grouped here ) , colocalizations and enzymatic reactions . even if enzymatic reactions are considered according to psi - mi standard as a subtype of direct interactions ,
there are counted here only as enzymatic reaction . the number of evidences by high throughput experiment and the number of evidences in which the two proteins are part of a larger complex are indicated in the last two columns .
each figure in the different columns is linked to the description of the evidences supporting the interaction . by clicking the 
22 link on the first row one obtains the information in the the left frame where the evidences for sh3kbp1 as a partner of cbl are grouped by publication and detection method . in the viewer applet
the network can be extended by clicking on the  +  symbol in the small circles ( it is possible to undo this operation by right clicking on the same symbol ) .
a protein can be removed from the displayed graph by right - clicking on it .
the size of the nodes and the distance between them can be controlled through the slide bars in the upper part of the graphic frame .
a third slide bar allows the user to hide interactions whose scores are below a chosen threshold . in the graphic display algorithm ,
the node repulsion force is proportional to the number of partners . as a consequence ,
two proteins with many interactors ( hubs ) will tend to lie further away in the graph display when compared with proteins with fewer partners .
this graph display rule facilitates the identification of hubs in the graph . as an additional feature , to help identify interaction partners in complex graphs , the action of clicking on a node brings all its partners forward and all the other nodes in the network decrease in size . only bait 
prey partners are represented in the viewer ( spoke model ) , but all components of the same complex are also brought forward during this operation .
any network displayed by the viewer can be exported as a list of protein pairs along with their confidence score ( button score ) , or in either psi - mitab and psi - mi xml format , both described later in this document .
the network exported in a standard psi - mi format may be easily imported and analyzed in visualization software such as cytoscape ( 23 ) . both the html page and the viewer applet are connected to relevant information in other pages of the mint website .
hyperlinks are provided to the source of the descriptions [ this information is imported from the uniprot knowledge base ( 24 ) ] or the full description of the interactions and the experiments by which they are supported .
a visit to the mint web - site typically starts by searching for a gene name , a protein name or a cross - reference [ to uniprotkb , refseq ( 25 ) , etc . ] .
if the protein is present in the mint database , the query returns an html page describing the protein on the left frame and listing the interactors in the right frame as described in the previous paragraph .
in addition to the information about the protein imported from uniprot , a list of ortholog proteins available in mint is appended .
if the protein is human or has a human ortholog , it is possible to switch to homomint , where the network of experimentally verified human protein interactions is extended with the interactions transferred from model organisms .
an additional page describes all the experimental details and provides a link to sister databases whenever the interaction is relevant for the specific topic .
sister databases offer several advantages , including additional data ( for instance inferred interactions , or interactions between  non - natural peptides and proteins ) and an interface adapted to the specific needs of the specialized database ( display of the modular structure of the proteins , visualization of viral - host networks ) . finally , a new tool .
this tool permits interrogation of the database with a list of proteins and returns the entire network of interactions connecting them .
the search is performed on a list of proteins cross - references ( for instance a list of uniprot accession numbers ) , and the user can choose whether to include in the network additional proteins that connect the query proteins ( figure 3 ) . since the algorithm underlying this tool is demanding up to 100 proteins can be submitted . 

the node size has been reduced to the minimum with the scrollbar to provide a lighter view of the network .
the node size has been reduced to the minimum with the scrollbar to provide a lighter view of the network .
all the entries in mint can be freely downloaded in several formats from a public ftp site , and are programmatically accessible through a web - service .
the former version of the psi - mi xml format ( 1.0 ) has been deprecated and it is no longer available for downloading .
the model is normalized , meaning that the experiments and interactors are not repeated in the interaction descriptions but are first listed and then referenced by the interactions . the normalized model results in lighter files .
the psi - mi xml format , in its complex structure , is not human readable but allows a complete description of molecular interactions and their experimental evidences .
one of the most relevant advantages is the possibility to associate more than two proteins with an interaction , allowing the correct representation of purified complexes , without misleading binary extensions .
additionally , features such as mutations , modifications or binding sites can be annotated with their sequence .
the ftp site for psi - mi xml export contains two directories : 
 pmids : a single file is generated for each publication in mint.datasets : containing xml files with the complete dataset or separate files describing interaction entries for each of the main model organisms ( human , yeast , fly and worm ) or a group of phylogenetically related organisms ( e.g. mammals ) . 

psi - mi xml files for large datasets containing more than 1000 interactions , such as those derived from manuscripts reporting high throughput experiments or datasets for intensively studied organisms , are split in smaller files and zipped together .
datasets : containing xml files with the complete dataset or separate files describing interaction entries for each of the main model organisms ( human , yeast , fly and worm ) or a group of phylogenetically related organisms ( e.g. mammals ) .
files in the psi - mitab format contain the same information , but in a tab - delimited format that can be opened in a spreadsheet software and it is easier to parse .
the columns of version 2.6 are the 15 columns of version 2.5 ( see http://code.google.com/p/psimi/wiki/psimitabformat ) extended with 16 new columns ( read discussion at http://code.google.com/p/psimi/issues/detail?id=2 ) .
an expansion strategy is applied in order to represent a complex of three or more proteins in a binary file format .
there are two models that can be adopted to achieve this goal . on one hand , matrix model
, one can represent the complex as the ensemble of all the possible binary interactions between the protein members .
alternatively , spoke model , one member of the complex ( bait ) can be associated to all the remaining members ( prey ) .
none of those models faithfully describes the topology of a complex , and the resulting protein pairs are not meant to represent the interaction between the protein in the complex . if the interaction on a row results from the expansion of a complex , the expansion mode ( spoke , matrix ) is specified in this field .
the field is empty if the binary interaction is not the result of an expansion procedure .
this allows the user to filter rows where the interaction is not supported by an experiment that is evidence for a binary interaction , or to reconstruct the complexes ( for instance by grouping rows by interaction identifier and looking at the experimental role of the components ) .
ppi databases , adhering to psi mi , have commonly agreed to use the spoke model as a method to represent n - ary interaction data in a binary format during the psi - mi 2009 spring meeting .
this means that if the experiment consists of the identification of many preys with a single bait ( i.e. as in tap tag technology ) , all possible bait  prey interactions are represented . if , on the other hand , the role of the proteins in the experiment supporting the existence of the complex is 
neutral ( i.e. in the case of a complex identified by purification by co - sedimentation ) , one protein is chosen as an  arbitrary bait . since we feel that this policy may be misleading for some user cases , we provide two files .
exploded according to the spoke model . there is no overlap between those two files , which can be appended one to the other to obtain the full dataset .
this issue is not relevant for xml files in which the representation of complexes is possible . in the last additional column , 
caution interaction , we export the caution annotations described in the previous paragraphs  for instance if an interaction is curated with mimix standards rather than fully adhering to the imex curation manual , or if a publication has been only partially curated .
finally , we provide a tab - delimited format , similar to mitab , where all the proteins forming a complex are described in a single line ( complexes are not exploded ) . in this format
we list the baits or enzymes ( for enzymatic reactions ) in the first column , and the preys or enzyme targets in the second .
web services allow the access to the data computationally and have become increasingly more popular in the bioinformatics community .
the hupo - psi workgroup has defined a standard web service to access molecular databases : the psicquic interface .
documentation about the psicquic interface , the psicquic providers and the reference implementation are available at http://code.google.com / p / psicquic/.
italian association for cancer research ( airc ) , telethon and the enfin fp7 network of excellence .
 mint ( http://mint.bio.uniroma2.it/mint ) is a public repository for molecular interactions reported in peer - reviewed journals . since its last report 
 , mint has grown considerably in size and evolved in scope to meet the requirements of its users . 
 the main changes include a more precise definition of the curation policy and the development of an enhanced and user - friendly interface to facilitate the analysis of the ever - growing interaction dataset . 
 mint has adopted the psi - mi standards for the annotation and for the representation of molecular interactions and is a member of the imex consortium . 
INTRODUCTION
ANNOTATION POLICY
LIGHT CURATION
SISTER DATABASES
A SCORING SYSTEM FOR INTERACTION CONFIDENCE
WEB INTERFACE
DATA AVAILABILITY
FUNDING