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README iRefIndex MITAB2.6 proposal for 7.0

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NoteNote

This is an expansion of the MITAB format that was proposed for use in iRefIndex 7.0 and subsequent releases; it does not correspond to any released product and is considered obsolete.

This proposal is based on the experimental form of the iRefIndex MITAB format found at...

http://irefindex.uio.no/wiki/README_iRefIndex_expanded_MITAB_proposal

  • Look for xxx or To do notes for things that need to be changed to create a version specific form of this README.
  • Look for Change notes for items that differ significantly from the current MITAB format.

This format is based on recent changes agreed upon by the PSI-MI working group in Turku, Finland.

References:

Last edited: 2010-10-19

Applies to iRefIndex release: none

Release date: never incorporated into a release

Download location: not available

Authors: Ian Donaldson, Sabry Razick, Paul Boddie

Database: iRefIndex (http://irefindex.uio.no)

Organization: Biotechnology Centre of Oslo, University of Oslo (http://www.biotek.uio.no/)

Note: this distribution includes only those data that may be freely distributed under the copyright license of the source database. See Description below.

Contents

Description

This file describes the contents of the

xxx

directory and the format of the tab-delimited text files contained within. Each index file follows the PSI-MITAB2.6 format with additional columns for annotating edges and nodes. Assignment of source interaction records to these redundant groups is described at http://irefindex.uio.no. The PSI-MI2.6 format plus additional columns is described below.

Details on the build process are available from the publication PMID 18823568.

There are two sets of data: free and proprietary. The free version includes only those data that may be freely distributed under the copyright license of the source database. This includes data from BIND, BioGRID, IntAct, MINT, MPPI and OPHID.

iRefIndex also integrates data from CORUM, DIP, HPRD and MPact. This data is not distributed publicly, but may be made available to academic users under a collaborative agreement.

Contact ian.donaldson at biotek.uio.no if you are interested in using the iRefIndex database or would like your database included in the public release of the index.

Sources http://irefindex.uio.no/wiki/Sources_iRefIndex_xxx
Statistics http://irefindex.uio.no/wiki/Statistics_iRefIndex_xxx
Download location ftp://ftp.no.embnet.org/irefindex/data/archive/xxx

Directory contents

README pointer to this file at http://irefindex.uio.no/wiki/README_iRefIndex_MITAB_xxx
Sources pointer to data files for this release at http://irefindex.uio.no/wiki/Sources_iRefIndex_xxx
Statistics pointer to statisitics for this release at http://irefindex.uio.no/wiki/Statistics_iRefIndex_xxx
xxxx.mitab.mmddyyyy.txt.zip individual indices in PSI-MITAB2.5 format

iRefIndex data is distributed as a set of tab-delimited text files with names of the form xxxx.mitab.mmddyyyy.txt.zip where mmddyyyy represents the file's creation date.

The complete index is available as All.mitab.mmddyyyy.txt.zip .

Taxon specific data sets are also available for:

Taxon Id
Homo sapiens 9606 (human)
Mus musculus 10090 (mouse)
Rattus norvegicus 10116 (brown rat)
Caenorhabditis elegans 6239 (nematode)
Drosophila melanogaster 7227 (fruit fly)
Saccharomyces cerevisiae 4932 (baker's yeast)
Escherichia coli. 562 (E. Coli)
Other other
All all

Taxon specific subsets of the data are named xxxx.mitab.mmddyyyy.txt.zip where xxxx is the taxonomy identifier of at least one of the interactors according to either the source interaction database or the sequence database record. Each zip compressed file contains a single text file with the corresponding name xxxx.mitab.mmddyyyy.txt.

In some cases, other objects may belong to other taxons if a virus-host interaction is being represented or if a protein from another organism has been used to model a protein in the specified organism.

Taxonomy identifiers are provided in the data sets allowing these exceptions to be identified. The taxonomy identifiers listed are derived from the source protein sequence record. In some cases, this taxonomy identifier will be a child of the taxon listed in the file's title; for example, Escherichia coli K12 (taxonomy identifier 83333) will appear in the Escherichia coli (taxonomy identifier 562) file.

A description of the NCBI taxon identifiers is available at the following location:

http://www.ncbi.nlm.nih.gov/sites/entrez?db=taxonomy

The above data taxon division scheme leads to duplications; for instance, an interaction present in the mouse index could also appear in the human index if the interaction record lists protein sequence records from both human and mouse. The All.mitab.mmddyyyy file is a complete and non-redundant listing.

The data format and divisions provided in this initial release were chosen in the hopes that they would be immediately useful to the largest possible set of users. Other formats and divisions are possible and we welcome your input on future releases.

Changes from last version

Sabry new {

  1. This version is comparable to the experimental centric version
  2. The way interactions involving more than one instance of a protein is changed. This will reflect much for homo-dimers, intramolecular interactions and homo-polymers. This change is due to the possibility of the original source providing an interaction between two isoforms of the same gene and canonicalization process wrongly representing this as homo-interaction.

The new representation is as follows.

  • When there is only one molecule provided as the interactor, both uidA and uidB will be this molecule and the edge type would be “Y” (please see column=50).
  • When there are two molecule of the same type or canonical iRefIndex procedure maps them to be so; both uidA and uidB will be this molecule and the edge type would be “X” (please see column=50).
  • when there are more than two molecule of the same type or canonical iRefIndex procedure maps them to be so; both uidA and uidB will be this molecule and the edge type would be “C” (please see column=50). Bipartite representation will be used in this case.

} xxx

Known Issues

xxx

Understanding the iRefIndex MITAB format

iRefIndex is distributed in PSI-MITAB format. Version 2.5 of the format was originally described in a recent PSI-MI paper (PMID 17925023, full text). The following summary shows the columns defined by version 2.6 of the format plus columns added by iRefIndex (italicised) grouped by entity type:

Entity type Principal columns Other columns
Experiment Method, author, pmids
Interaction Before_C13N_rigid interactionType, sourcedb, interactionIdentifiers, confidence, edgetype, numParticipants
Interactor Final_ROGID_A, Final_ROGID_B taxA, taxB, interactor_type_A, interactor_type_B, OriginalReferenceA, OriginalReferenceB, FinalReferenceA, FinalReferenceB
Canonical interaction Checksum_Interaction, C13N_rig
Canonical interactor Checksum_A, Checksum_B, irogA, irogB uidA, uidB, altA, altB, aliasA, aliasB

Since this PSI-MITAB format allows for only two interactors to be described on each line, it is best suited for describing binary interaction data (the original experiment, say yeast two hybrid, gives a binary readout). However, other source PSI-MI XML source records will describe interactions involving only one interactor type (dimers or multimers) or they will contain associative (also known as "n-ary") interaction data from, for example, immunoprecipitation experiments where the exact interactions between any pair of interactors are unknown. These cases are problematic for the PSI-MITAB format. This document describes exactly how we use the MITAB format to describe these alternate (non-binary) interaction types.

What each line represents

Each line or row in the MITAB file represents a single interaction record from one primary data source describing an interaction involving the exact same set of proteins (as defined by their primary sequence and taxonomy identifiers).

NoteChange

Previously, each line represented a group of interaction records.

A single interaction is described on a separate line since this allows us to convey additional information about each of the original source records. Users can still "collapse" or find all lines that describe an interaction between the same set of proteins by using the "RIG" (column 47) or "RIGID" (column 35 or 48). Rows with identical rigids (redundant interaction group identifiers) all describe interactions between the same set of proteins.

The natural keys for each interaction record in this group (that is, the record identifiers from the source database) are listed under interactionIdentifier (column 14). For example:

intact:EBI-761694
NoteChange

Our surrogate (primary) key for a group of redundant interaction records (RIG) is no longer listed in column 14; only the source database record is listed in this column. The RIG identifier is now listed (by itself) in column 48 (and column 35 in canonical form).

The RIG identifier is a 27 character key that is derived from the ROGIDs of the interactors involved in the interaction record (see columns 41 and 42). The RIG identifier is listed (by itself) in column 48 for convenience. The ROGID is a SHA-1 digest of the protein interactor's primary amino acid sequence concatenated with the NCBI taxonomy identifier (see the paper for details).

Representation of interactions

Sometimes source interaction records in PSI-MI format only list one interactor. These are cases where either 1) an intramolecular interaction is being represented or 2) a multimer (3 or more) of some protein is being represented. These records are difficult to represent in the PSI-MITAB format because PSI-MITAB requires that each row (interaction) list two interactors. The way we handle this is to list the ROG identifier for the single interactor twice (once in each of columns 41 and 42) of the MITAB. The RIG identifier for these interactions will be the SHA-1 digest of the interactor’s ROG id (see column 48). These interactions are marked by a Y in column 50.

Note that column 50 may also contain a C. This indicates that the MITAB entry describes membership of a protein in some complex. These entries correspond to PSI-MI records where more than two interactors are listed (associative interaction data; a.k.a. n-ary data cf. binary data). In these cases, the first column holds the ROG identifier of the complex and the second column contains the ROG id of the protein. We refer to this method of representation as a bi-partite model since there are two kinds of nodes corresponding to complexes and proteins.

As an example, let’s say that a source interaction record contained interactors A, B and C found by affinity purification and mass-spec where a tagged version of protein A was used as the bait protein to perform the immunoprecipitation.

Then we would represent the complex in the MITAB file using three lines:

X-A
X-B
X-C

All three entries would have the same string in column 35 or 48 (the RIG id for the complex). All three entries would have a C in column 50.

Other databases take an interaction record with multiple interactors (n-ary data) and make a list of binary interactions (based on the spoke or matrix model) and then list these binary interactions in the MITAB. For the example above, using a spoke model to transform the data into a set of binary interactions, these data would be represented using two lines in the MITAB file:

A-B
A-C

Here A is chosen as the "hub" of the spoke model since it was the "bait" protein. For experimental systems that do not have "baits" and "preys" (such as X-ray crystallography), an arbitrary protein might be chosen as the bait.

Alternatively, a matrix model might be used to transform the n-ary data into a list of binary interactions. Here all pairwise combinations of interactors in the original n-ary data are represented as binary interactions. So, in the above example, the immunoprecipitated complex would be represented using three lines of the MITAB file: A-B, B-C, and A-C.

All three methods for representing n-ary data in a MITAB file (bi-partite, spoke, and matrix) are different representations of the same data.

We have chosen to use the bi-partite method of representation so that it is impossible to mistake spoke or matrix binary entries for true binary entries; the identifiers used for complexes will, of course, not appear in a protein database and any programme that tries to treat complex identifiers as though they were protein identifiers will fail. The method allows you to reconstruct the members of the original interaction record that describes a complex of proteins (say from an affinity purification experiment). From there, you can choose to make a spoke or matrix model by yourself if you want.

Users are advised that other databases will use spoke and matrix model representations of complexes. In these cases, column 50 will indicate this fact. The pairs of proteins found in these entries do not necessarily represent observations of real binary interactions: they merely represent membership in some larger list of proteins observed to be somehow associated.

For binary interaction data, column 50 will contain an X. Two protein interactor ROGIDs will be listed in columns 33 and 34 (and also in columns 41 and 42).

Canonical interactors and interactions

As indicated by the summary table given above, the MITAB format used by iRefIndex now contains information about interactors and interactions that use canonicalized information as described in the Canonicalization document. Since each line refers to a specific, observed interaction (column 48) and specific interactors (columns 41 and 42), information about the canonical groups involved in an interaction (columns 33 and 34, also columns 43 and 44) and the resulting canonical interaction (column 35, also column 47) provides an additional layer which can be used to group specific interactions.

Thus, in the file, a collection of interactions "labelled" with this additional layer of canonical information would resemble the following:

CA-CB A1-B1 CI I1
CA-CB A1-B2 CI I2
CA-CB A2-B2 CI I3

Here, CA is the canonical group for A1 and A2, and CB is the canonical group for B1 and B2. Since CA and CB remain the same for all of the specific interactions listed above, the canonical ROGID will also remain the same in the form of CI, even though the specific interactions between combinations of A1, A2, B1 and B2 produce the distinct ROGIDs I1, I2 and I3.

Canonical group coverage

Note that the MITAB file will not necessarily provide all members of a given canonical object group - that is, all ROGIDs corresponding to a given canonical ROGID - since the file only contains observed interactions. Although a ROGID may be mapped to a canonical ROGID, if the specific ROGID is never observed in an interaction, it will never be listed in this file. Consequently, any attempt to find the theoretical size of a canonical group - the number of proteins potentially represented by a particular canonical ROGID - will fail where such non-interacting ROGIDs exist. This file can only provide the size of a canonical group in terms of interacting proteins.

  • To find the size of a canonical group in terms of its interacting members, all distinct ROGIDs corresponding to a particular canonical ROGID can be collected, regardless of the interactions in which they participate.
  • By considering canonical interactions, the number of interacting members of a canonical group can be found for each canonical interaction. Note that this figure is typically less than the total number of interacting members for any given canonical group.

License

Data released on this public ftp site are released under the Creative Commons Attribution License http://creativecommons.org/licenses/by/2.5/. This means that you are free to use, modify and redistribute these data for personal or commercial use so long as you provide appropriate credit. See next section.

iRefIndex data distributed on the FTP site includes only those data that may be freely distributed under the copyright license of the source database. This includes data from BIND, BioGRID, IntAct, MINT, MPPI and OPHID.

iRefIndex also integrates data from CORUM, DIP, HPRD and MPact. These data are not distributed publicly. These data may be made available to academic users under a collaborative agreement.

Contact ian.donaldson at biotek.uio.no if you are interested in using the iRefIndex database or would like your database included in the public release of the index.

Copyright © 2008-2010 Ian Donaldson

Citation

Credit should include citing the iRefIndex paper (PMID 18823568) and any of the source databases upon which this resource is based. See http://irefindex.uio.no for appropriate citations.

Disclaimer

Data is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.

Description of PSI-MITAB2.6 file

Each line in this file represents either

  1. an interaction between two proteins (binary interaction) or
  2. the membership of a protein in some complex (complex membership) or
  3. an interaction that involves only one protein type (multimer or self-interaction).

See column 50 for more details.

Column number: 1 (uidA)

Column type: String
Description: Unique identifier for the canonical group to which interactor A belongs.
Example:
uniprotkb:P23367

Notes


This column contains an identifier, taken from a major database, for a protein representing the canonical group to which interactor A belongs. i.e select one identifier from a list of identifiers used by all the sources to represent any member of the canonical group. The user should not assume that this provided identifier is the one participating in the interaction, this is just a selected identifier to represent the canonical group. Due to the way original sources provide identifier, this field may contain:

  1. Identifiers of wrong format : (e,g RefSeq:NP 036076 instead of RefSeq:NP_036076)
  2. Version information (e.g. GenBank:AAN15193.1)
  3. Wrong database (e.g. GenBank:NP_013133 instead of RefSeq:NP_013133)
  4. Structural identifier which are not referring to the full sequence ("PDB:1OCC|I")
  5. Incomplete identifiers ("PDB:1KQ1| ")
  6. Outdated or deleted identifier (UniProt:Q9H233 instead of UniProt:Q29RF6)

It should also be noted that “OriginalReferenceA” (Column number: 38) may or may not match what is given in this column.

But it is guaranteed that a canonical group would be always represented by the same identifier.

Column number: 2 (uidB)

Column type: String
Description: Unique identifier for the canonical group to which interactor B belongs.
Example:
uniprotkb:P06722

Notes

See notes for column 1.

Column number: 3 (altA)

Column type: Pipe-delimited set of strings
Description: Alternative identifiers for interactor A
Example:
uniprotkb:P23367|refseq:NP_418591|entrezgene/locuslink:948691

Notes

NoteChange

Previously, this column listed database identifiers for specific interactors. Since column 1 (and column 33) now refers to a canonical group, this column lists interactors for all members of that group.

Column 3 lists database names and accessions that belong to the same canonical group. Members of a canonical group do not all necessarily have the same sequence (although they all belong to the closely related taxon). Members of a canonical group may include splice isoform products from the same or related genes. One member of the canonical group is chosen to represent the entire group. The identifier for that canonical representative is listed in column 43.

Each pipe-delimited entry is a database_name:accession pair delimited by a colon. Database names are taken from the MI controlled vocabulary at the following location:

http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI

Database references listed in this column may include the following:

uniprotkb
The accessions this protein is known by in UniProt (http://www.uniprot.org/). More information regarding this protein can be retrieved using this accession from UniProt. See the AC line in the flat file. http://au.expasy.org/sprot/userman.html#AC_line.
refseq
If a protein accession exists in the RefSeq data base (http://www.ncbi.nlm.nih.gov/RefSeq/) that reference is indicated here. More information about this protein can be obtained from RefSeq using this accession.
entrezgene/locuslink
NCBI gene Identifiers for the gene encoding this protein. See ftp://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2refseq column GeneID given protein's accession.version
other
If none of the three identifier types are available then other databasename:accession pairs will be listed. These database names may not follow the MI controlled vocabulary.

Example:

emb:CAA44868.1|gb:AAA23715.1|gb:AAB02995.1|emb:CAA56736.1|uniprot:P24991
irefindex
If the node represents a complex, then the rogid for the complex will be listed here, such as the following:
irefindex:xBr9cTXgzPLNxsaKiYyHcoEm/DM

Column number: 4 (altB)

Column type: Pipe-delimited set of strings
Description: Alternative identifiers for interactor B
Example:
uniprotkb:P06722|refseq:NP_417308|entrezgene/locuslink:947299

Notes

See notes for column 3.

Column number: 5 (aliasA)

Column type: Pipe-delimited set of strings
Description: Aliases for interactor A
Example:
uniprotkb:MUTL_ECOLI|entrezgene/locuslink:mutL

Notes

Each pipe-delimited entry is a database name:alias pair delimited by a colon. Database names are taken from the PSI-MI controlled vocabulary at the following location:

http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI

Database names and sources listed in this column may include the following:

uniprotkb:entry name
the entry name given by UniProt. See the description for "Entry name" in the section of http://au.expasy.org/sprot/userman.html#ID_line concerning the "ID (IDentification)" line of the flat file
entrezgene/locuslink:symbol
the NCBI gene symbol for the gene encoding this protein. See the section in ftp://ftp.ncbi.nlm.nih.gov/gene/README for gene_info, specifically details for the Symbol column
irefindex:complex
If the node is a complex then irefindex:complex will be listed here.
NA
NA may be listed here if aliases are not available

Column number: 6 (aliasB)

Column type: Pipe-delimited set of strings
Description: Aliases for interactor B
Example:
uniprotkb:MUTH_ECOLI|entrezgene/locuslink:mutH

Notes

See notes for column 5.

Column number: 7 (Method)

Column type: String
Description: Interaction detection method
Example:
MI:0039(2h fragment pooling)

Notes

NoteChange

Only a single method will appear in this column. Previously, multiple methods appeared.

Both the controlled vocabulary term identifier for the method (e.g. MI:0399) and the controlled vocabulary term short label in brackets (e.g. 2h fragment pooling) will appear in this column. See http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI to look up controlled vocabulary term identifiers.

The interaction detection method is from the original record. Path for PSI-MI 2.5:

entrySet/entry/experimentList/experimentDescription/interactionDetectionMethod/names/shortLabel/


NoteChange

If a controlled vocabulary term identifier was not provided by the source database then an attempt was made to use the supplied short label to find the correct term identifier. If a term identifier could not be found, then MI:0000 will appear before the shortLabels.

NA or -1 may appear in place of a recognised shortLabel.

For example:

MI:0000(-1)
MI:0000(NA)

Column number: 8 (author)

Column type: Pipe-delimited set of strings
Description:
Example:
hall-1999-1|hall-1999-2|mansour-2001-1|mansour-2001-2|hall-1999

Notes

According to MITAB2.5 format this column should contain a pipe-delimited list of author surnames in which the interaction has been shown.

NoteChange

This column will usually include only one author name reference. However, some experimental evidences have secondary references which could be included here.

Column number: 9 (pmids)

Column type: Pipe-delimited set of strings
Description: PubMed Identifiers
Example:
pubmed:9880500|pubmed:11585365

Notes

This is a non-redundant list of PubMed identifiers pointing to literature that supports the interaction. According to MITAB2.5 format, this column should contain a pipe-delimited set of databaseName:identifier pairs such as pubmed:12345. The source database name is always pubmed.

NoteChange

This column will usually include only one PubMed reference that describes where the experimental evidence is found. In some cases, secondary references will be included here.


The special value - may appear in place of the identifiers.

Column number: 10 (taxa)

Column type: Pipe-delimited set of strings
Description: Taxonomy identifier for canonical interactor A
Example:
taxid:83333(Escherichia coli K-12)

Notes

The NCBI taxonomy identifier listed here is that of the sequence record for the interactor and may be different than what is listed in the interaction record. See the methods section for more details. See also the NCBI taxonomy database at the following location:

http://www.ncbi.nlm.nih.gov/sites/entrez?db=taxonomy

According to the MITAB2.5 format, this column should contain a pipe delimited set of databaseName:identifier pairs such as taxid:12345. The source database name has been listed as taxid since it is always NCBI's taxonomy database. The value in this column will be NA if the interactor is a complex.

Column number: 11 (taxb)

Column type: Pipe-delimited set of strings
Description: Taxonomy identifier for canonical interactor B
Example:
taxid:83333(Escherichia coli K-12)

Notes

See notes for column 10.

Column number: 12 (interactionType)

Column type: String
Description: Interaction Type from controlled vocabulary or short label
Example:
MI:0218(physical interaction)

Notes

NoteChange

Only one interaction type will be present in each line of the file (previously, multiple types were listed).

The interaction type is taken from the PSI-MI controlled vocabulary and represented as...

database:identifier(interaction type)

...(when available in the interaction record) or Path for PSI-MI 2.5:

entrySet/entry/interactionList/interaction/interactionType/names/shortLabel

See http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI to lookup controlled vocabulary term identifiers for interaction types.

NoteChange

If the MI controlled vocabulary identifier was not provided by the source database, but a text description was provided, then an attempt was made to map the text to the correct controlled vocabulary term identifier. If this was not possible then MI:0000 is listed.

NA may be listed here if the interaction type is not available (meaning that we could not find the interaction type in the record provided by the source database).

Column number: 13 (sourcedb)

Column type: String
Description: Source databases containing this interaction
Example:
MI:0469(intact)

Notes

Taken from the PSI-MI controlled vocabulary and represented as...

database:identifier(source name)

See http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI to lookup controlled vocabulary term identifiers for database sources.

NoteChange

Only one source database will be listed in each row.

Column number: 14 (interactionIdentifier)

Column type: String
Description: source interaction database and accession
Example:
intact:EBI-761694

Notes

Each reference is presented as a database name:identifier pair.

NoteChange

Only one source database reference will be listed in each row. The RIGID (from iRefIndex) is no longer listed in this column. See column 35 instead.

The source database names that appear in this column are taken from the PSI-MI controlled vocabulary at the following location (where possible):

http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI

If an interaction record identifier is not provided by the source database, this entry will appear as database-name:- with the identifier region replaced with a dash (-).

Column number: 15 (confidence)

Column type: Pipe-delimited set of strings
Description: Confidence scores
Example:
lpr:1|hpr:12|np:1

Notes

Each reference is presented as a scoreName:score pair. Three confidence scores are provided: lpr, hpr and np.

PubMed Identifiers (PMIDs) point to literature references that support an interaction. A PMID may be used to support more than one interaction.

The lpr score (lowest pmid re-use) is the lowest number of distinct interactions (RIGIDs, see column 35) that any one PMID (supporting the interaction in this row) is used to support. A value of one indicates that at least one of the PMIDs supporting this interaction has never been used to support any other interaction. This likely indicates that only one interaction was described by that reference and that the present interaction is not derived from high throughput methods.

The hpr score (highest pmid re-use) is the highest number of interactions (RIGIDs, see column 35) that any one PMID (supporting the interaction in this row) is used to support. A high value (e.g. greater than 50) indicates that one PMID describes at least 50 other interactions and it is more likely that high-throughput methods were used.

The np score (number pmids) is the total number of unique PMIDs used to support the interaction described in this row.

- may appear in the score field, indicating the absence of a score value.


NoteChange

COLUMNS PAST THIS POINT (16 - 31) ARE PART OF THE NEW PSI-MITAB 2.6 FORMAT

Column number: 16 (expansion)

Column type: String
Description: Model used to convert n-ary data into binary data for purpose of export in MITAB file
Example:
bipartite

Notes

For iRefIndex, this column will always contain either bipartite or none.

Other databases may use either spoke or matrix or none in this column.

See Understanding the iRefIndex MITAB format for an explanation.

Column number: 17 (biological_role_A)

Column type: String
Description: Biological role of interactor A
Example:
MI:0501(enzyme)

Notes

When provided by the source database, this includes single entries such as MI:0501(enzyme), MI:0502(enzyme target), MI:0580(electron acceptor), or MI:0499(unspecified role).

See http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI to browse possible values for biological role.

For complexes and when no role is specified this column will indicate an unspecified role.

Column number: 18 (biological_role_B)

Column type: String
Description: Biological role of interactor B
Example:
MI:0501(enzyme)

Notes

See notes for column 17.

Column number: 19 (experimental_role_A)

Column type: String
Description: Indicates the experimental role of the interactor (such as bait or prey).
Example:
MI:0496(bait)
Example:
MI:0498(prey)

Notes

This column indicates the experimental role (if any was provided by the source database) that was played by interactor A (columns 1, 33, 41).

See http://www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MI to see definitions of bait and prey. as well as browse other possible values of experimental role that may appear in this column for other databases.

For complexes and when no role is specified this column will contain the following:

MI:0499(unspecified role)

Column number: 20 (experimental_role_B)

Column type: String
Description: Indicates the experimental role of the interactor (such as bait or prey).
Example:
MI:0496(bait)
Example:
MI:0498(prey)

Notes

This column indicates the experimental role (if any) that was played by interactor B (columns 2, 34, 42).

See notes above for column 19.

Column number: 21 (interactor_type_A)

Column type: String
Description: describes the type of molecule that A is
Example:
MI:0326(protein)

Notes

For iRefIndex, this will always be one of...

MI:0326(protein)
MI:0315(protein complex)

Column number: 22 (interactor_type_B)

Column type: String
Description: describes the type of molecule that B is
Example:
MI:0326(protein)

Notes

See column 21.

Column number: 23 (xrefs_A)

Column type: Pipe-delimited set of strings
Description: xrefs for molecule A
Example:
omim:152430(longevity)|go:"GO:0016233"(telomere capping)

Notes

This is not used by iRefIndex. A dash (-) will always appear in this column.

This column may be used to list cross-references to annotation information for molecule A. For example, Gene Ontology identifiers or OMIM identifiers.

Column number: 24 (xrefs_B)

Column type: Pipe-delimited set of strings
Description: xrefs for molecule A
Example:
-

Notes

This is not used by iRefIndex. A dash (-) will always appear in this column.

See notes to column 23.

Column number: 25 (xrefs_Interaction)

Column type: Pipe-delimited set of strings
Description: xrefs for the interaction
Example:
go:"GO:0048786"(presynaptic active zone)

Notes

This is not used by iRefIndex. A dash (-) will always appear in this column.

This column may be used to list cross-references to annotation information for the interaction. For example, Gene Ontology identifiers or OMIM identifiers.

Column number: 26 (Annotations_A)

Column type: Pipe-delimited set of strings
Description: Annotations for molecule A
Example:
This protein has an apparent MW of 25 kDa|This protein binds 7 zinc molecules

Notes

This is not used by iRefIndex. A dash (-) will always appear in this column.

This column may be used to list free-text annotation information for the interaction.

Some databases may use dataset:* or data-processing:* (where * is non-controlled free-text) in this column.

Column number: 27 (Annotations_B)

Column type: String
Description: Annotations for molecule B
Example:
-

Notes

This is not used by iRefIndex. A dash (-) will always appear in this column.

See notes to column 26.

Column number: 28 (Annotations_Interaction)

Column type: Pipe-delimited set of strings
Description: Annotations for interaction
Example:
figure-legend:F1A|prediction score:432|comment:prediction based on phage display consensus|author-confidence:8|comment:AD-ORFeome library used in the experiment.

Notes

This is not used by iRefIndex. A dash (-) will always appear in this column.

This column may be used to list free-text annotation information for the interaction. The keys used before the : (like "comment") are database specific and not controlled.

Some databases may use dataset:* or data-processing:* (where * is non-controlled free-text) in this column.

Column number: 29 (Host_organism_taxid)

Column type: String
Description: The taxonomy identifier of the host organism where the interaction was experimentally demonstrated
Example:
taxid:10090(Mus musculus)

Notes

This may differ from the taxonomy identifier associated with the interactors. Other possible entries are:

  • taxid:-1(in vitro)
  • taxid:-4(in vivo)

A dash (-) will be used when no information about the host organism is available.

taxid:32644(unidentified) will be used when the source specifies the host organism taxonomy identifier as 32644.

Column number: 30 (parameters_Interaction)

Column type: String
Description: Parameters for the interaction
Example:
-

Notes

This is not used by iRefIndex. A dash ( - ) will always appear in this column.

Internal note : use of this column is not well-defined or characterized.

Column number: 31 (Creation_date)

Column type: String (yyyy/mm/dd)
Description: When was the entry created.
Example:
2010/05/06

Notes

This will be the release date of iRefIndex for all entries in this file.

This date will not match the date for the corresponding record in the source database.

Column number: 32 (Update_date)

Column type: String (yyyy/mm/dd)
Description: When was this record last updated?
Example:
2010/05/06

Notes

This will be the release date of iRefIndex for all entries in this file.

This date will not match the date for the corresponding record in the source database.

Column number: 33 (Checksum_A)

Column type: String
Description: Unique identifier for the canonical group to which interactor A belongs. Column 43 is an integer equivalent to this identifier.
Example:
crogid:hhZYhMtr5JC1lGIKtR1wxHAd3JY83333

Notes

NoteChange

This column contains a universal key for the canonical group to which interactor A belongs.

Column 3 lists database names and accessions that belong to this group. Members of a canonical group do not all necessarily have the same sequence (although they all belong to the same taxon). Members of a canonical group may include splice isoform products from the same or related genes. One member of the canonical group is chosen to represent the entire group. The identifier for that canonical representative is listed in this column.

See http://irefindex.uio.no/wiki/Canonicalization for a description of canonicalization. Protein references from the original interaction record can be found in columns 37 and 38 as well as in the corresponding iRefWeb record. See column 47 for an integer identifier that can be used to search for this interaction record at http://wodaklab.org/iRefWeb/.

This universal key listed here is the ROGID (redundant object group identifier) described in the original iRefIndex paper. PMID 18823568. However, an additional round of processing called canonicalization (C13N) has been performed before choosing a protein to represent this interactor. Therefore this identifier may differ from the value in column 41 (the final ROGID before canonicalization).

If this line (entry) describes a binary interaction between two proteins, then the protein whose ROGID is sorted last (in ascending ASCII-based lexicographical sort order) is listed as interactor A (in column 33) and uidA (column 1).

If this entry describes the membership of a protein in a complex, then the ROGID of the complex is always listed first as interactor A and the member protein's ROGID is listed second as interactor B; see Checksum_B (column 34) and uidB (column 2)).

If this entry describes a an interaction involving only one protein type, then the ROGID of that protein is listed for both interactor A and B.

The ROGID (redundant object group identifier) for proteins, consists of the SEGUID for the protein concatenated with the taxonomy identifier for the protein. For complex nodes, the ROGID is calculated as the SHA-1 digest of the ROGIDs of all the protein participants (after first ordering them by ASCII-based lexicographical sorting in ascending order and concatenating them) See the iRefIndex paper for details. The SEGUID is always 27 characters long. So the ROGID will be composed of 27 characters concatenated with a taxonomy identifier for proteins.

Column number: 34 (Checksum_B)

Column type: String
Description: Unique identifier for the canonical group to which interactor B belongs. Column 44 is an integer equivalent to this identifier.
Example:
crogid:AhmYiMtz8lR12Gixt91txbAd3JY83333

Notes

See notes for column 33.

Column number: 35 (Checksum_Interaction)

Column type: String
Description: Redundant interaction group identifier involving canonical groups
Example:
crigid:3ERiFkUFsm7ZUHIRJTx8ZlHILRA

Notes

The Canonical RIGID (for redundant interaction group identifier) consists of the canonical (C13N) ROG identifiers for each of the protein participants (see notes above) ordered by ASCII-based lexicographic sorting in ascending order, concatenated and then digested with the SHA-1 algorithm. See the iRefIndex paper for details. This identifier points to a set of redundant protein-protein interactions that involve the same set of proteins with the exact same primary sequences.

Column number: 36 (Negative)

Column type: Boolean (true or false)
Description: Does the interaction record provide evidence that some interaction does NOT occur.
Example:
false

Notes

This value will be false for all lines in this file since iRefIndex does not include "negative" interactions from any of the source databases.


COLUMNS PAST THIS POINT (37 -) ARE NOT DEFINED BY THE PSI-MITAB2.6 STANDARD. THESE COLUMNS ARE SPECIFIC TO THIS IREFINDEX RELEASE AND MAY CHANGE FROM ONE RELEASE TO ANOTHER

Column number: 37 (OriginalReferenceA)

Column type: database name:accession
Description: Database name and reference used in the original interaction record to describe interactor A
Example:
uniprotkb:P23367

Notes

NoteChange

This column corresponds in part to the altA column in the previous format, since it refers to specific information about the first interactor, although only a single reference is provided instead of the list of references previously found in altA.

This is the protein reference that was found in the original interaction record to describe interactor A. It is a colon-delimited pair of database name and accession. It may be either the primary or secondary reference for the protein provided by the source database.

For complexes this will be the ROGID of the complex.

Column number: 38 (OriginalReferenceB)

Column type: database name:accession
Description: Database name and reference used in the original interaction record to describe interactor B
Example:
uniprotkb:P23367

Notes

See notes for column 37.

Column number: 39 (FinalReferenceA)

Column type: database name:accession
Description: Database name and reference used in the updated/final interaction record to describe interactor A
Example:
uniprotkb:P23367

Notes

The difference between “OriginalReferenceA” (Column number: 37) and FinalReferenceA is the OriginalReferenceA is what was found in the original record and FinalReferenceA is what was used by the assignment and processing algorithm. The FinalReferenceA will defer in following instances from the OriginalReferenceA,

  1. The original reference is of wrong format (e,g RefSeq:NP 036076 instead of RefSeq:NP_036076).
  2. Incomplete identifiers provided by OriginalReferenceA (PDB:1KQ1| , missing chain information).
  3. Outdated or deleted identifier provided by OriginalReferenceA(UniProt:Q9H233 ), the FinalReferenceA will be the latest available accession in this case.
  4. The OriginalReferenceA is ambiguous.(i.e GeneId) FinalReferenceA will be a protein product selected in a systematic way in this case.

Column number: 40 (FinalReferenceB)

Column type: database name:accession
Description: Database name and reference used in the updated/final interaction record to describe interactor B
Example:
uniprotkb:P23367

Notes

See notes for column 39.

Column number: 41 (Final_ROGID_A)

Column type: String
Description: Unique identifier for interactor A. Before canonicalization (C13N).
Example:
rogid:hhZYhMtr5JC1lGIKtR1wxHAd3JY83333

Notes

NoteChange

This column contains a universal key for the interactor. It corresponds to the ROGID (redundant object group identifier) described in the original iRefIndex paper BEFORE canonicalization has been performed, as described in PMID 18823568.

Protein references from the original interaction record (and a description of how they were mapped to the final form and then to the canonical form) can be found in the corresponding iRefWeb record. See column 47 and search for this interaction record at http://wodaklab.org/iRefWeb/.

Column number: 42 (Final_ROGID_B)

Column type: String
Description: Unique identifier for interactor B. Before Canonicalization.
Example:
rogid:hhZYhMtr5JC1lGIKtR1wxHAd3JY83333

Notes

See notes for column 41.

Column number: 43 (irogA)

Column type: Integer
Description: Unique identifier for the canonical group to which interactor A belongs.
Example:
irefindex:2345

Notes

NoteChange

This column contains an internal, integer key for the canonical group to which interactor A belongs.

A alphanumeric equivalent of this key (that can be generated by anyone, and is thus universal) appears in column 33. See the notes for column 33 for more details on how protein identifiers were mapped from the original database record to this key.

Column 3 lists database names and accessions that belong to this group. Members of a canonical group do not all necessarily have the same sequence (although they are all associated with the same organism). Members of a canonical group may include splice isoform products from the same or related genes. One member of the canonical group is chosen to represent the entire group. The identifier for that canonical representative is listed in this column.

The identifier listed here is stable from one release of iRefIndex to another starting from release 6.0.

Column number: 44 (irogB)

Column type: Integer
Description: Unique identifier for the canonical group to which interactor B belongs.
Example:
irefindex:456543

Notes

See notes for column 43.

Column number: 45 (MappingScoreA)

Column type: String
Description: String describing operations performed by iRefIndex procedure during mapping from original protein reference (columns 37, 38) to the final protein reference (columns 39, 40). This score is not referring to uidA. This is because uidA may not be the used accession
Example:
PTUO+

Notes

This column contains a description of mapping operations as a condensed string of letters. See the original iRefIndex paper, PMID 18823568. Protein references from the original interaction record (and a description of how they were mapped to the canonical form) can also be found in the corresponding iRefWeb record. See column 47 and search for this interaction record using the following service:

http://wodaklab.org/iRefWeb/

For complexes the column will provide the following value:

-

This value is preferred to NA since the latter resembles a sequence of scoring operations.

Column number: 46 (MappingScoreB)

Column type: String
Description: String describing operations performed by iRefIndex procedure during mapping from original protein reference (columns 37, 38) to the final protein reference (columns 39, 40). This score is not referring to uidB. This is because uidB may not be the used accession
Example:
SU

Notes

See notes for column 45.

Column number: 47 (C13N_rig)

Column type: String
Description: Redundant interaction group
Example:
crig:12345

Notes

This is an internal, integer equivalent of the canonical RIGID. See column 35.

This integer may be used to query the iRefWeb interface for the interaction record. For example:

http://wodaklab.org/iRefWeb/interaction/show/13653

...where 13653 is the canonical RIG.

Starting with release 6.0, this canonical RIG is stable from one release of iRefIndex to another.

Column number: 48 (Before_C13N_rigid)

Column type: String
Description: Redundant interaction group identifier - before canonicalization (C13N).
Example:
rigid:3ERiFkUFsm7ZUHIRJTx8ZlHILRA

Notes

The RIGID (for redundant interaction group identifier) consists of the ROG identifiers for each of the protein participants (see notes above) ordered by ASCII-based lexicographic sorting in ascending order, concatenated and then digested with the SHA-1 algorithm. See the iRefIndex paper for details. This identifier points to a set of redundant protein-protein interactions that involve the same set of proteins with the exact same primary sequences.

The rigid is constructed from ROGs before canonicalization. This identifier can be easily and universally constructed by data providers to facilitate data integration and exchange.

Column number: 49 (imex_id)

Column type: String
Description: IMEx identifier if available
Example:
imex:IM-12202-3
Example:
When no information available a dash will be used ( - )

Notes

Column number: 50 (edgetype)

Column type: Character
Description: Does the edge represent a binary interaction (X), member of complex (C) data, or a multimer (Y)?
Example:
X

Notes

Edges can be labelled as either X, C or Y:

X
a binary interaction with two protein participants
C
denotes that this edge is a binary expansion of interaction record that had 3 or more interactors (so-called "complex" or "n-ary" data). The expansion type is described in column 16 (expansion). In the case of iRefIndex, the expansion is always "bipartite" meaning that Interactor A (columns 33, 41) of this row represents the collection of interactors and Interactor B (columns 34, 42) represents a protein that is a member of this group.

See Understanding the iRefIndex MITAB format for further explanation.

Y
for dimers and polymers. In case of dimers and polymers when the number of subunits is not described in the original interaction record, the edge is labelled with a Y. Interactor A (columns 33, 41) will be identical to the Interactor B (columns 34, 42). The graphical representation of this will appear as a single node connected to itself (loop). The actual number of self-interacting subunits may be 2 (dimer) or more (say 5 for a pentamer). Refer to the original interaction record for more details and see column 51.

Column number: 51 (numParticipants)

Column type: Integer
Description: Number of participants in the interaction
Example:
2

Notes

  • For edges labelled X (see column 50) this value will be two.
  • For edges labelled C, this value will be equivalent to the number of protein interactors in the original n-ary interaction record.
  • For interactions labelled Y, this value will either be the number of self-interacting subunits (if present in the original interaction record) or 1 where the exact number of subunits is unknown or unspecified.
NoteImportant

The number of participants can be greater than the number of distinct proteins involved in an interaction because a single protein can participate more than once in an interaction. Such participation is enumerated and counted to produce the value in this column.