IMEx Data Submission

 

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Data Submission

The IMEx consortium actively encourages the deposition of data, prior to publication, and will supply unique accession numbers which may be referenced within the final article. A data privacy policy prior to final publication is maintained by all databases. Submitters may send their data directly to any of the member databases using a variety of formats listed below, but should all conform to the following guidelines as to the minimum information required to describe the data.

IMEx accession numbers suitable for inclusion in a publication will normally be issued within five working days after receipt of all necessary data. 

 

Minimum Data Requirements

IMEx partner databases request the following minimum information about a molecular interaction experiment to be provided with each data deposition. Submitters should supply the following information.

1. Manuscript information

·       Contact email

·       Publication title

·       First author

·       Publication identifier

 

2. Experiment

Experimental procedures should be described in detail, preferably using the controlled vocabulary terms produced by the Human Proteome Organization Proteomics Standards Initiative (HUPO-PSI). These are available on the PSI web site or the Ontology Lookup Service. To include:

·       Host system (NCBI taxid and details of tissue, cell line…)

·       Interaction detection method

·       Participant detection method

 

3. Interaction

·       Participant – to be identified by either molecule identifiers from a public domain database or a sequence accompanied by species of origin (NCBI taxid).

Protein accession number from UniProtKB, RefSeq, or a model organism database
Gene identifiers from Ensembl, Entrez Gene, a model organism database or nucleotide accession number from DDBJ, EMBL, GenBank.
Small molecules should be described with full chemical names of accession number from ChEBI or PubChem.

·         Biological role of each participant (e.g. enzyme)

·         Experimental role of each participant (e.g. bait)

 

4. Confidence

If applicable, a confidence value attributed to the interaction.

 

Data Submission by e-mail

Several databases will accept submissions in free text format, for example a manuscript prepared for submission. Please send your submission to your database of choice.

 

Data Submission by PSI-MI Interchange Format

Producers of large datasets may wish to submit their data in the form of XML files, following the PSI-MI standard for molecular interactions. The current version is 2.5.

Files should then be sent to any of the participating databases listed above. It may be useful to view the following example of a validated file containing minimal information but we would encourage the addition of any further experimental detail which is available.

 

Data Submission by Excel Sheet

For biologists who wish to submit data in a structured form but do not wish to produce an XML file, a Microsoft Excel© submission sheet has been prepared.

Please note:

 this spreadsheet will not operate correctly on the Apple Mac version of Microsoft Excel©

 this spreadsheet makes use of Visual Basic macros to allow it to connect to the Ontology Lookup Service to retrieve the latest PSI-MI ontology terms and to allow it to select the correct ontology term accessions, this making it easy for you to select the correct terms to annotate your data.

For your security, we have signed the VBA in this spreadsheet with a digital certificate issued by Thawte™. When you first open the spreadsheet you will be presented with one of the following two dialogue boxes, depending on the current security setting in your version of Excel.

 


If security level is set to ‘High’, you must tick 'Always trust macros from this source'
and then click ‘Enable Macros’.


If security level is set to ‘Medium’, you can simply click ‘Enable Macros’,
however it is recommended that you first tick 'Always trust macros from this source'.
Macros will then be automatically enabled for this spreadsheet when you open it in the future.

 

Once you have accepted the certificate, the spreadsheet will proceed to the update of its controlled vocabularies. You will be prompted the following message box beforehand:

 

If the 'Update PSI-MI CV Terms' dialogue box does not appear, you will not be able to enter data on to the spreadsheet as the necessary macros are disabled. If this occurs, or if you encounter any other problems, please report to .

 

Files should then be sent to any of the participating databases listed above. It may be useful to view the following example of a validated file containing minimal information but we would encourage the addition of any further experimental detail which is available.

 

Data Submission by Web Form

For users who prefer to use a structured web form to add data, such a tool has been built which allows the user to move successively through the submission process, listing the experiments, interactors and interactions as described above.

 

Files should then be sent to any of the participating databases listed above.

 

Data Submission - a Worked Example

To aid in data deposition the following publication is represented in the multiple forms offered for IMEx data deposition, to provide a reference example:

 

Croze, E., Usacheva, A., Asarnow, D, Minshall, R.D., Perez, H.D., Colamonici O
PubMed ID: 11046044

 

Receptor for activated C-kinase (RACK-1), a WD motif-containing protein, specifically associates with the human type I IFN receptor.

J Immunol. 2000 Nov 1;165(9):5127-32.

 

The data is available in:

 

Full annotation of the data in this paper can be viewed in the IntAct database at www.ebi.ac.uk/intact using Accession Nos.

 

Release Policy

All IMEx partners agree to release submitted data only when accepted by a peer reviewed journal for publication and not before the date of publication of the corresponding paper. The data will be made public by the database to which it was submitted and released as an IMEx record which may be included in the datasets of any or all IMEx databases.