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Database of Interacting Proteins
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DIRECT DIP/IMEx SUBMISSIONS
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We are always looking for authors willing to directly deposit
peer-reviewed protein interaction data into DIP. Whereas, so far,
the majority of data in DIP have been entered into the database by
trained DIP curators or imported from other members of the IMEx
consortium we strongly encourage the authors of the primary
experimental data to directly submit their results into DIP and,
in effect, into all the other databases participating in IMEx.
Besides making the data rapidly available to the research
community it would ensure the results are accuratly described with
proper identification given to each interacting protein - in our
experience unabmigious and accurate identification of the proteins
used in each experiment is the most time consuming and error-prone
step in the curation process, often resulting in the rejection of
otherwise valuable interaction data.
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To submit interaction data to DIP, follow these two easy steps:
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- Format the data (using one of the tools below; MIF 2.5 XML files are preferred)
- Email us
the formatted data file
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If you run into trouble, we are happy to help -- email us at
dip@mbi.ucla.edu.
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As we realize that describing interaction data in a highly structured
format required by the IMEx agreement is not a simple task we provide
access to a number of tools co-developed by the members of the IMEx
consortium as well as by the HUPO-PSI community in hope to make the
process as simple and user friendly as possible.
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Data Preparation Tools
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FormIt |
A simple, Web-based tool that can be used to prepare files
in MIF 2.5 format which are readily accepted by all IMEx partners.
FormIt, reminiscent of GenBank's BankIt pages guides the user through
preparation of files containing only the very basic description of the
interaction data, as defined in the MIMIx paper. It is suitable
for preparation of files describing a small number of interactions
reported in a typical paper targeting few interactions of one or
more proteins.
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MIMIx Template | Submission sheet that can be used to prepare
interaction data in a structured form from within the familar
Microsoft Excel spreadsheet program. Excel documents prepared with the
template alre also readily accepted by all the IMEx partners. This mode
of data preparation is desired when larger interaction datasets are
pr the author decides to provide more experimental details than it is
possible within FormIt pages.
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Useful links
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OLS Site |
EBI's Ontology Lookup Service (OLS) site provides access to the most recent
controlled vocabulary terms that shoud be used to annotate the interaction
data.
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MIF Utilities |
Some simple utilities, useful when preparing MIF 2.5 files. MIF viewer
displays the contents of a MIF file in a human-readable format, MIF
syntax checker provides information about file conformance to the
formal MIF 2.5.3 syntax specification.
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Copyright 1999-2017 UCLA. All DIP database records available through this Web Site are freely available under the terms set by the Creative Commons Attribution-NoDerivs License. This means that you are free to copy, distribute, display and make commercial use of these databases in all legislations, provided you give us credit. However, if you intend to distribute data from our database, you must ask us for permission first.
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