Minimum Data Requirements
IMEx partner databases request the following minimum information about a molecular interaction experiment to be provided with each data deposition. Data should be MIMIx compatible. 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
- 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.
4. Experimental role of each participant (e.g. bait/prey)
5. Confidence If applicable, a confidence value attributed to the interaction.
IMEx databases will take datasets of any size - from a single interaction to a high throughput experiment with many thousands of interactions or participating molecules. In order for us to correctly annotate the data, it is helpful for us to also be sent the accompanying manuscript, which need not be in its final form, but will enable us to ensure we have captured all the infromation you intend to publish. As with the data, all information in the manuscript will be kept confidential until the date of publication.
Data Submission by e-mail
Several databases will accept submissions in free text format, for example a manuscript prepared for submission. Either send an e-mail to Contact us alerting us to your data and we will decide on the most apporpirate database and help with data preparation of contact one of the below directly.
- IntAct (www.ebi.ac.uk/intact), please send to email@example.com
- DIP (http://dip.doe-mbi.ucla.edu), please send to firstname.lastname@example.org
- MINT (http://mint.bio.uniroma2.it/mint), please send to email@example.com
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, we are happy to receive data by Excel spreadsheet in the author's own format, providing the MIMIx-specific details requested above are included in the sheet. Please note that IMEx databases capture full details of binding domains, tags etc so all such data should be included either in the sheet or in an accomapnying manuscript.
If your data consists only of a small number of interactions, it may be simpler just to send a copy of the relevant manuscript and accompanying figures.
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.