| Feb 13, 2017 |
| Yet another set of protein-protein interactions has been released. It covers interaction
data from more than 8,200 research publications. More than 5,400 of these have been curated
following IMEx Consortium
curation rules.
|
| Feb 4th, 2014 |
| We have just released a long-overdue update to our
MiSink plugin. It now supports
the most recent production version of Cytoscape
(3.0.x series) as well as upcoming Cytoscape 3.1.x series (now in beta testing: see
latest successful build on code.cytoscape.org page.
|
| Jan 17th, 2014 |
| We are pleased to release another set of protein-protein interactions. It adds data from
more than 600 publications curated according to the
IMEx Consortium
curation rules. It also includes
recurated data from one of the early large-scale studies
[Butland et al. (2005);
PMID:15690043] updated to IMEx-level standards.
Please, note that the latter update resulted in an apparent drop in the number of experiments reported in DIP.
This is because the initially curated dataset repoted each binary bait-prey interaction as demonstrated by
separate, independent experiment wheras the updated one reports these as inferences based on spoke expansions
of a smaller number of multi-protein affinity complexes.
|
| Oct 31st, 2013 |
| Another set of protein-protein interactions has arrived. With interactions added from more than 400 articles it is now based
on information retrieved from more than 6,500 research publications. More than 3,500 of these has been has been curated
according to the IMEx Consortium curation rules.
|
| July 7th, 2013 |
| Another set of protein-protein interactions has been released. It is based on information
retrieved from more than 6,000 research publications. More than half of these has been
has been curated according to the IMEx Consortium
curation rules.
|
| February 11th, 2013 |
| We have just released updated interaction datasets that reflect the state of the database as of
Jan 31, 2013. The DIP database contains now more than 75,000 distinct interactions based on
information extracted from nearly 5,900 research papers. More than 2,800 of these has been curated
according to the IMEx Consortium
curation rules. The original IMEx curation
records for these can be downloaded from
here.
|
| May 18th, 2012 |
| Another dataset release after adding interaction data from 101 papers. See our
statistics page for further details.
|
| February 28th, 2012 |
| New dasets has been released. They contain more then 73,000 interactions curated out of more then
5,200 research papers. See our statistics page for further details
and split between different organisms.
|
| January 10th, 2010 |
| We have just released a set of experimental, high-throughput interactions published last year
by Hu et al (2009). The dataset,
currently available from our IMEx export directory
(file: 2010-01-09.xml.gz),
will be incorporated into the next DIP data release. We would like to thank Javier Diaz and all
other members of the Emili Lab for direct data
submission and for providing us with additional information about the experiments.
|
| December 30th, 2009 |
| The recurated high throughput datasets have been incorporated into the most recent release of
the DIP data. The datasets are available from our download pages
(full dataset,
species subsets,
updated protein sequence file).
|
| December 21st, 2009 |
| As agreed with other members of the IMEx Consortium,
we have released the high throughput datasets published by
Ito 2001 et al.,
Ho 2002 et al. and
Gavin 2002 et al..
The datasets, available from our IMEx export directory
(ftp://dip.mbi.ucla.edu/imex/2009), conform
to the IMEx curation standard and will be incorporated shortly into our upcoming full dataset
release. The IMEx-compliant files include description of the original experimental data
and, when available, sets of computationally processed interactions provided by the authors.
The latter, annotated as inferred by author
(PSI-MI MI:0363 controlled
vocabulary term) to distinguish them from the original experimental data, are provided to
simplify their analysis and comparision with other, more recent datasets.
|
| February 7th, 2004 |
| We are pleased to provide cross-references leading from DIP nodes to the ProLinks database
of inferred functional linkages. The ProLinks database, at present, contains over 10 million
computationally inferred linkages in more than 80 genomes. Please follow the
DIP-6873N
link to sample the newly available information.
At the same time, following the advice of the database users, we've cleaned up a little DIP
user interface as well as added Gene Ontology consortium-based annotation of DIP nodes
(see eg
DIP-310N
).
|
| January 5th, 2004 |
| Another year (BTW Happy New Year to all ;o), another high-throughput dataset
made it into DIP. It was just published by Li et al. in Science (so
far only on-line; see
ScienceExpress, 2 January 2004).
As the two previous high-throughput data sets this one is also available for
all to
download.
Enjoy !
|
| November 25th, 2003 |
| After a bit of struggle to clean it up a little, the newest high-throughput
dataset provided by Giot et al
[PubMed]
has been incorporated into DIP. It is also available for all to
download in
both XIN and tab-delimited versions.
We anticipate the remaining high-throughput datasets to be available for
downloading soon.
We are also pleased to reveal the first in the series of additions and
improvements to the DIP web interface - an enhanced version of the
evidence details pages. At the moment, these are most noticable for
the Giot et al. data, such as
this one.
Please feel free to send us email
with comments & suggestions as we always appreciate feedback.
|
| April 18th, 2003 |
| Another full dataset release. Species-specific files are also there. Enjoy.
|
| January 5th, 2003 |
| The new DIP release is here once more. This time we provide not only the
full dataset file but also species-specific subsets in both
XINand
tab-delimited
formats.
|
| December 31st, 2002 |
| We are pleased to release a new (and, hopefully, improved) version of the DIP
database. Although most of the changes took invisibly place at the back-end.
For those technically-inclined: we've completed the migration from mySQL to
PostgreSQL database engine; this change was accompanied by a complete redesign
of the database. The changes will allow us to add, in the nearest future,
more user-visible features. However, some changes/addisions are already
available. Most prominently, we've incorporated the link validation information
to all the tables (eg
DIP:1143N)
and graphs (eg
DIP:1143N))
listing interactions
of S. cerevisiae proteins. Please, note the color coding used to distinguish between
the core/non-core links. This information was also used to 'uncrowd'
the graph representation of the interaction neighbourhood and make those
more usable. We hope the changes will make the database more useful to all
of you and, as always, anxiously wait for
comments and suggestions. Oh, and last
but not least, we've modified DIP logo (obviously taking inspiration from
here ;o);
|
| June 17th, 2002 |
| The initial XML based release of the complete set of DIP interactions is
here. It reflects the status of the database as of June 16 and contains
nearly 18,000 distinct protein-protein interactions identified in more
than 21,000 unique experiments. The switch to the
XIN format will ultimately allow us
to provide access to the details of the experimental data and also to
incorporate the results of the data quality assesment analysis.
We are also pleased to introduce an updated version of the edge
view pages (eg.
DIP:2562E)
that now provide a detailed information on the results of the quality
assesment described in
Deane, Salwinski at al..
|
| January 24th, 2002 |
| Another release of the complete dataset. It contains more than 11,000
individual protein-protein interactions described in 1,800 research papers.
Please, note that this is, most probably, the last dataset released in the
old format as we anticipate the next one (to be released witin ~3-4 months;
we'll try to prepare at least 3 updates a year) will be XML formatted.
|
| December 31st 2001 |
| The New Year's Eve upgrade to the web site.
First, we're pleased to introduce improvements to our
node search
page. Searching for a known protein is much easier now, as one can use, within
Node ID field, references to a number of other databases including, but
not limited to, SwissProt (both, accession numbers and entry names), PIR, NCBI
(any accession number and/or GI code recognized within NCBI system), SGD, YPD,
Pfam, ProDom, InterPro, etc. It is also possible to use logical expressions
when searching through some of the local annotation fields. Please, see the
Search Guide
for details.
We've also added a large number of cross-references to the
DIP Node pages - just find your preferred protein to check what's present
in the new cross-reference field. The cross-references are not,
per se, a part of DIP (therefore, they will not be included in the flat
file releases) but, nonetheless, we find them quite useful when browsing
through the database. The P, D, and F categories correspond, respectively, to
information about entire (P)roteins, (D)omains and sequence (F)eatures.
|
| November 2nd 2001 |
| Coming soon: LiveDIP, a sub-database of DIP which documents biological
interactions. Biological Interactions are a subset of DIP's physical
interactions, in which the state of one or both interacting partners undergoes
a transition to a new state. Biological Interactions are prominent in
signaling pathways where the state change often is a covalent modification of
one of the interacting partners. LiveDIP aims at gathering state of proteins
and their known transitions during Biological Interactions.
|
| October 22nd 2001 |
| The
Database of Ligand-Receptor Partners (DLRP) has been added to DIP. The
DLRP is a database of protein ligand and protein receptor pairs that are
known to interact with each other.
By interact we mean that the ligand and receptor are members of a
ligand-receptor complex and, unless otherwise noted, transduce a signal.
Currently DLRP consists mainly of human ligands and receptors, including
cytokines, chemokines, and growth, angiogenesis and developmental factors.
The DLRP has been applied to the bioinformatic identification of potential
autocrine signaling loops in cancers using gene expression data
(Graeber T.G. and
Eisenberg D.
Nature Genetics.
vol 29 no 3 pp296-300).
|
| September 5th 2001 |
| The new DIP release is here. It contains 10,432 interactions and 5,868
proteins. Some 500 interactions are from genome wide screen of these new
microbes. It contains a list of interactions from Helicobacter pylori.
This information are minimal (mainly giving only the two partners of the
interactions). To find more information you should go onto
Hybrigenics who generated these data.
They give more informations on domains and the interacting regions.
We only have what has been published by Rain et al.
Finally go onto the Download page to retrieve the whole dataset and enjoy the
DIP.
|
| July 5th 2001 |
| A long time without news. The new dataset should be available by the beginning
of next week and will contain 9746 interactions among 5703 proteins.
We also are ready to release a stand-alone program called JDIP
(Java 2 application) which allows one to manipulate, save, and
query protein interaction databases. This application also allows
users to save and record their own protein interaction datasets.
You can find the program
here. We hope you will enjoy this tool and that it will make your
experience in the protein interaction world easier.
|
| January 16th 2001 |
| Hi everybody perhaps you have seen a new button popping up on the Search Page.
A purple button which enables you to view interactions in a more active way
(actually Javactive). So we hope this tool will be useful for you (we are
using it to curate the database and find problems ! We would be very happy for
any comments or questions or improvement you would like to send an email to
jdip@mbi.ucla.edu. Otherwise the
article in NAR2001 is published (please refer to it).
|
| December 10th 2000 |
| A very long time without any news. So here it is we have decided to update the
data that you could download
here on this server.
The statistics so far are 3602 interactions. We hope you will like this new
release but please send us any errors or problems with the data that you might
encounter we really appreciate feedback ! Another thing a new NAR paper will
be publish in January so if you use the datababase please reference the new
article.
|
| September 18th 2000 |
| For a long time we have tried to provide a graphical tool to visualize protein
network contained in DIP. Today we introduce the first version we will upgrade
continuously this tool in order to provide more flexibility. We hope this will
help you place your protein of interest in its interaction network. The tool
can be accessed using the "blue" ball present in the Searching Webpage. Please
feel free to send us email we always appreciate feedback
|
| August 24th 2000 |
| Some news: we went to the ISMB2000 and many questions were asked about DIP.
Particularly one regarding the possibility to paste any sequences (FASTA
format) and obtained an interaction network. We will implement this in the
near future (hopefully before the end of the year). A new release of the
database should be available in the middle of September which, hopefully, will
contain more than 3108 interactions. And finally many persons wanted a FASTA
file of all protein sequences contained in DIP this will be available in the
next release.
|
| June 7th 2000 |
| You might or might not have seen this but now each and every SWISSPROT entry
on the official SWISSPROT site have been
hyperlinked to DIP. This will hopefully increase the number of users of DIP
and potentially also trigger some interest in adding new information to the
database. Once more if you have any information regarding protein-protein
interactions send us an e-mail.
|
| April 19th 2000 |
| A review has been published about DIP you could find it here
DIP review. One
of the main complain is the annotation problem which we all know is a
essential issue in database we are working on it. You will also observe a new,
green ball in the interaction information, by clicking on it a list of
interacting partners centered on your protein appears. You could now browse
through the network of interaction in a hopefully much easy way. Any comments
are as usual welcome DIP mail.
|
| March 8th 2000 |
| New flat files have been generated dip030800.dat is
a 2.6Mb database which contains 2151 protein-protein interactions. Mostly
these interactions have been generated from two hybrid assay and should be
taken with a lot of caution.
|
| January 5th 2000 |
| The paper describing the DIP database can be found at here
Nucleic Acids Research Vol 28 Issue 1 : January 2000. If you want to
publish or use data from this database please refer to this paper.
|
| October 21st 1999 |
| There it is three files have been generated and can be downloaded in the
Download page. The format of each file are hopefully clear enough and any perl
programmer would be happy (we hope). Contact us if you have any comments
Webmaster.
|
| September 28th 1999 |
| The new search engine support wild card * and ?, hope to be
useful to you. The upper part contains a general search on all fields of the
database. The bottom is a field by field search. You could combine all the
fields together in order to narrow your Search
|
| September 24th 1999 |
| Some fixing of the database has been performed on some fields. We have added
links to the ENZYME database. A new search engine will pop up probably next
week. For any question or error report send an email to
DIP mail.
|
| September 15th 1999 |
| Submission has been added to the menu list. Anybody interested in adding
information to DIP should contact us.
|
| August 26th 1999 |
| It is now possible to enter Swissprot/Genpept/PIR accession code.
Protein protein interaction in the past have been entered exclusively with PIR
accession code. Since this make DIP completely dependent on one database a
move towards Swissprot and Genpept accession code has been adopted. Quality of
an interaction can be assessed by the number of experimental methods. Since
many experiments could describe a protein-protein interaction one could test
the validity of an interaction by analyzing the methods involved. Each
experiments will be linked to the NCBI Medline Database.UID/PMID code are used
as a code to reference each published paper. By linking DIP to the NCBI/NLM
Medline Database, scientist can access in a easy way
|
