iRefIndex Release Notes

iRefIndex 20.0

August 2023 - release is prepared in the week of 28th of August

• Note: The data for the PSICQUIC web service will be released end of September 2023.

• This release of iRefIndex was assembled by Alexander Botzki at VIB Technologies in Belgium. See https://irefindex.vib.be/

• A psciquic web-service has been set up at https://irefindex.vib.be/webservices/

• The complete data set can be downloaded from this site README and Download

• This public distribution includes data consolidated using the iRefIndex method for BIND, BAR, BioGRID, CORUM, DIP, InnateDB, IMEX, IntAct, HPRD, HuRi, MATRIXDB, MPACT, MPPI and MPIDB, REACTOME, VIRUSHOST, UNIPROTPP, HPIDB, BHF-UCL, and QuickGO.

• Release 20.0 contains 161,166 new distinct interaction records since release 19.0

• All of these resources have been integrated from freely available sources. See the sources links below for details.

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See the MITAB format description for a complete list of changes and issues related to MITAB output.

(README and Download, Sources, Statistics)

iRefIndex 19.0

August 2022

• Note: The data for the PSICQUIC web service will be released end of November 2022.

• This release of iRefIndex was assembled by Luc Ducazu at the VIB Bioinformatics core in Belgium with support and guidance from James Collier and Alexander Botzki. See https://irefindex.vib.be/

• A psciquic web-service has been set up at https://irefindex.vib.be/webservices/

• The complete data set can be downloaded from this site README and Download

• This public distribution includes data consolidated using the iRefIndex method for BIND, BAR, BioGRID, CORUM, DIP, InnateDB, IntAct, HPRD, HuRi, MATRIXDB, MPACT, MPPI and MPIDB, REACTOME, VIRUSHOST, UNIPROTPP, HPIDB, BHF-UCL, and QuickGO.

• Release 19.0 contains 378,321 new distinct interaction records since release 18.0

• All of these resources have been integrated from freely available sources. See the sources links below for details.

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See the MITAB format description for a complete list of changes and issues related to MITAB output.

(README and Download, Sources, Statistics)

iRefIndex 18.0

June 2021

• Note: The data for the PSICQUIC web service will be released end of August 2021.

• This release of iRefIndex was assembled by Tom Nissens at the VIB Bioinformatics core (https://www.bits.vib.be/) in Belgium with support and guidance from Shoshana Wodak and Alexander Botzki. See https://irefindex.vib.be/

• A psciquic web-service has been set up at https://irefindex.vib.be/webservices/

• The complete data set can be downloaded from this site README and Download

• 5659 interactions for SARS-CoV-2 are available here: https://irefindex.vib.be/psicquic/webservices/current/search/query/taxid:2697049

• This public distribution includes data consolidated using the iRefIndex method for BIND, BAR, BioGRID, CORUM, DIP, IntAct, HPRD, HuRi, MATRIXDB, MPACT, MPPI and MPIDB, REACTOME, VIRUSHOST, UNIPROTPP, HPIDB, MOLCON, BHF-UCL, Spike, and QuickGO.

• Release 18.0 contains 83,146 new distinct interaction records since release 17.0

• All of these resources have been integrated from freely available sources. See the sources links below for details.

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See the MITAB format description for a complete list of changes and issues related to MITAB output.

(README and Download, Sources, Statistics)

iRefIndex 17.0

June 2020

• This release of iRefIndex was assembled by Joris Dekimpe at the VIB Bioinformatics core (https://www.bits.vib.be/) in Belgium with support and guidance from Shoshana Wodak and Alexander Botzki. See https://irefindex.vib.be/

• A psciquic web-service has been set up at https://irefindex.vib.be/webservices/

• The complete data set can be downloaded from this site README and Download

• 605 interactions for SARS-CoV-2 are available here: https://irefindex.vib.be/psicquic/webservices/current/search/query/taxid:2697049

• This public distribution includes data consolidated using the iRefIndex method for BIND, BioGRID, CORUM, DIP, IntAct, HPRD, MATRIXDB, MPACT, MPPI and MPIDB, REACTOME, VIRUSHOST, UNIPROTPP, HPIDB, MOLCON, BHF-UCL, Spike, and QuickGO. New data sources include BAR and HuRI.

• Release 17.0 contains 218,642 new distinct interaction records since release 16.0

• All of these resources have been integrated from freely available sources. See the sources links below for details.

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See the MITAB format description for a complete list of changes and issues related to MITAB output.

(README and Download, Sources, Statistics)

iRefIndex 16.0

June 2019

• This release of iRefIndex was assembled by Sam Dupont at the VIB Bioinformatics core (https://www.bits.vib.be/) in Belgium with support and guidance from Shoshana Wodak and Alexander Botzki. See https://irefindex.vib.be/

• A psciquic web-service has been set up at https://irefindex.vib.be/webservices/

• The complete data set can be downloaded from this site README and Download

• This public distribution includes data consolidated using the iRefIndex method for BIND, BioGRID, CORUM, DIP, IntAct, HPRD, MATRIXDB, MPACT, MPPI and MPIDB. New data sources include INTACT COMPLEXES, I2D_IMEX, REACTOME, VIRUSHOST, UNIPROTPP, HPIDB, MOLCON, BHF_UCL, MBINFO, Spike, and QuickGO.

• Release 16.0 contains 310,640 new distinct interaction records since release 15.0

• All of these resources have been integrated from freely available sources. See the sources links below for details.

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See the MITAB format description for a complete list of changes and issues related to MITAB output.

(README and Download, Sources, Statistics)

iRefIndex 15.0

January 2018

• This release of iRefIndex was assembled by Alexander Botzki at the VIB Bioinformatics core (https://www.bits.vib.be/) group in Belgium and Andrei Turinsky at the Hospital for Sick Children in Toronto, Canada with support and guidance from Shoshana Wodak and Ian Donaldson. See https://irefindex.vib.be/

• A psciquic web-service has been set up at https://irefindex.vib.be/webservices/

• The complete data set can be downloaded from this site README and Download

• This public distribution includes data consolidated using the iRefIndex method for BIND, BioGRID, CORUM, DIP, IntAct, HPRD, MATRIXDB, MPACT, MPPI and MPIDB. MINT is now included in IntAct. New data sources include INTACT COMPLEXES, I2D_IMEX, REACTOME, VIRUSHOST, UNIPROTPP, HPIDB, MOLCON, BHF_UCL and MBINFO.

• Release 15.0 contains 169,271 new distinct interaction records since release 14.0

• All of these resources have been integrated from freely available sources. See the sources links below for details.

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See the MITAB format description for a complete list of changes and issues related to MITAB output.

(README and Download, Sources, Statistics)

iRefIndex 14.0

April 2015

• This public distribution includes data consolidated using the iRefIndex method for BIND, BioGRID, CORUM, DIP, IntAct, HPRD, MATRIXDB, MPACT, MPPI and MPIDB. MINT is now included in IntAct.

• BIND_TRANSLATION, and INNATEDB are not included due to mapping problems during the build process. These may be returned in a later release. OPHID is permanently removed.

• An extended version is available only to clients of Donaldson Research and includes new data sources: INTACT COMPLEXES, I2D_IMEX, REACTOME, SPIKE, VIRUSHOST, UNIPROT, HPIDB, MOLCON, BHF_UCL and MBINFO. If you are interested in working with these data in the context of iRefIndex, please contact ian@donaldsonresearch.com.

• All of these resources have been integrated from freely available sources. See the sources links below for details.

• Integer identifiers for interactors and interactions are only applicable to the current release - they cannot be used to find an interactor or interaction n a previous release. These integer identifiers include irogida, irogidb, irigid, icrogida, icrogidb and icrigid.

• The extended version of release 14.0 contains 231,324 new distinct interaction records since release 13.0

---

Known issues that bear repeating based on recent questions

See the MITAB format description for a complete list of changes and issues related to MITAB output.

(README and Download, Sources, Statistics)

iRefIndex 13.0

December 2013

• MINT records are now distributed by IntAct.

• All records created by the MINT database are now distributed from the IntAct web-site and FTP site. All MINT interaction records have been assigned an EBI identifier as the record's primary identifier. The original MINT record identifier is preserved as a secondary identifier in the records distributed by IntAct. However, only the EBI identifier is provided in iRefIndex and the source is always listed as IntAct.

• md5 checksum files are now included in download directories.

• release 13.0 contains 20460 new distinct interaction records since release 12.0

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Known issues that bear repeating based on recent questions

• Interactions involving small molecules are missing

iRefIndex indexes only those interaction records where ALL of the interactors are proteins. This means that records involving small molecules and proteins will not be indexed. The number of such records is growing mostly due to curation efforts of IntAct and Reactome - the inclusion of interactions involving small molecules will be considered for a future release.

• Missing genetic interactions

The majority of genetic interactions were removed as of release 10. This was intentional but the change was not noted in this change-log section. The primary source of genetic interactions was the BioGRID database - close to 200 thousand records.

• More details on known issues

See the MITAB format description for a complete list of changes and issues related to MITAB output.

(README and Download, Sources, Statistics)

iRefIndex 12.0

June 2013

• Release 12 corrects the appearance of RefSeq chromosome identifiers that first appeared in release 10 and were used (erroneously) to refer to protein interactors.

• As of November 30th, 2011, the MINT database produced its last release in PSI-XML format (ftp://mint.bio.uniroma2.it/pub/release/psi/) and now only releases data in PSI-MITAB format (ftp://mint.bio.uniroma2.it/pub/release/mitab26/). The most recent MINT release at the time of writing was from May 20th, 2013. This means that many MINT records are missing from iRefIndex. A new parser will be written to accomodate the PSI-MITAB MINT format for a future release of iRefIndex.

• See the MITAB format description for a complete list of changes and issues related to MITAB output.

Thanks to Paul Boddie for bug fixes.

(README and Download, Sources, Statistics)

iRefIndex 11.0

May 2013

• Release 11 corrects the appearance of deprecated Entrez Gene Ids found in version 10. This build also includes a module to update iRefWeb.

See the MITAB format description for a complete list of changes related to MITAB output.

Thanks Andrei Turinsky, Lilian Hanna and Paul Boddie for testing and bug fixes.

README_MITAB2.6_for_iRefIndex

(README and Download, Sources, Statistics)

iRefIndex 10.0

March 2013

• Release 10 was built using a pipeline rewritten by Paul Boddie to simplify the build process and reduce build time

See the MITAB format description for a complete list of changes related to MITAB output.

Thanks to Aleksandar Stojmirovic, Andrei Turinsky and Thomas Schmitt for early testing.

(Sources, Statistics)

iRefIndex 9.0

November 2011

• RIGIDs in previous releases of iRefIndex were incorrectly computed. Although the properties of such RIGIDs were not compromised - distinct RIGIDs should still have referred to distinct interactions - each RIGID made use of substantially less information from its components. RIGIDs in this release should now be computed correctly. (Internal link)
• Many proteins previously assigned the 4932 taxonomy identifier have been recategorised as having taxonomy identifier 559292. Thus, for convenience, an additional 559292 file is produced alongside the existing (but substantially smaller) 4932 file to hold interactions involving proteins associated with both taxons. (Internal link)

See the MITAB format description for a complete list of changes related to MITAB output.

New data sources: InnateDB, MatrixDB, MPI-LIT, MPI-IMEX

(Sources, Statistics)

iRefIndex 8.0

January 2011

See the MITAB format description for a complete list of changes related to MITAB output.

(Sources, Statistics)

iRefIndex 7.0

May 2010

• This is the first release to use the PSI-MITAB2.6 format.

See the MITAB format description (and MITAB 2.5 format description) for a complete list of changes related to MITAB output.

New sources: BIND Translation

Removed sources: I2D

(Sources, Statistics)

iRefIndex 6.1

February 2010

• This release fixed a problem in iRefIndex 6.0 related to MPPI interactions spuriously being provided as evidence.

See the MITAB format description for a complete list of changes related to MITAB output.

(Sources, Statistics)

iRefIndex 6.0

October 2009

• The "arbitrary" method for choosing a protein interactor when the identifier provided by the source database could be interpreted as one of multiple different proteins has been changed to consult certain sequence databases in order.

See the MITAB format description for a complete list of changes related to MITAB output.

(Sources, Statistics)

iRefIndex 5.1

August 2009

• This release fixed errors in iRefIndex 5.0.

See the MITAB format description for a complete list of changes related to MITAB output.

(Sources, Statistics)

iRefIndex 5.0

July 2009

New sources: I2D

See the MITAB format description for a complete list of changes related to MITAB output.

(Sources, Statistics)

iRefIndex 4.0

June 2009

See the MITAB format description for a complete list of changes related to MITAB output.

(Sources, Statistics)

iRefIndex 3.0

March 2009

New sources: CORUM

See the MITAB format description for a complete list of changes related to MITAB output.

(Sources, Statistics)

iRefIndex 2.0

October 2008

New sources: BIND, BioGRID, DIP, HPRD, IntAct, MINT, MPACT, MPPI, OPHID

See the MITAB format description for a complete list of changes related to MITAB output.

(Sources, Statistics)

iRefIndex 1.1

July 2008

• The method used to select the largest SEGUID was modified, thus changing some ROG identifiers.
• The method used for RIGID calculation was also changed from previously generated data.
• The iRefIndex publication describes the methods used in this release.

See the MITAB format description for a complete list of changes related to MITAB output.

All iRefIndex Pages

Follow this link for a listing of all iRefIndex related pages (archived and current).