International Protein Index (Ipi)

Question

[Varun Gupta]

Hi Everyone

I have a list of ribosomal protein genes and i want to extract the corresponding IPI (International Protein Index) for it.

How can i get them for all the genes in one go?

Hope to hear from you guys soon.

Regards Varun

[Khader Shameer]

I am wondering why you want to use IPI in your analysis ? IPI is deprecated by EBI, you could use an alternate resource for your analysis.

Answer 1

[Vikas Bansal]

Download IPI Gene Cross-References File Format from here. The description of file format is here. You can download the file. I think 6th or 7th column is gene name and 10th column is IPI. You can extract your interest of genes with IPI's.

[Louis]

The last release is here. That file format description has been taken down too, but was last archived here.

Column     Summary                  Comments
1          Chromosome               Values: 1-n (where n = 22 (human), 19 (mouse), 20
                                    (rat), etc..), W, X, Y, Z, "M" for Mitochondrion,
                                    "C" for Chloroplast, "Un" for unknown.
2          Cosmid                   For some Ensembl genes, a location in the complete
                                    chromosome is not known owing to the incompletion
                                    of the underlying sequence assembly, and the 
                                    co-ordinates provides are merely the local
                                    co-ordinates within a single cosmid. Where
                                    this is the case, the cosmid name is given 
                                    in the second column
3          Start co-ordinate        Given in base pairs, global (these are chromosomal
           of gene (on              co-ordinates, except in cases discussed previously).
           Ensembl assembly).       Data taken from Ensembl. 
4          End co-ordinate          Given in base pairs, global (these are chromosomal 
           of gene (on              co-ordinates, except in cases discussed previously).
           Ensembl assembly).       Data taken from Ensembl.
5          Strand of gene           1 for FORWARD or SENSE and -1 for REVERSE or
           (on Ensembl              ANTISENSE.
           assembly)
           corresponding to
           these co-ordinates.     
6          Gene location            Taken from species-specific gene resource (e.g. HUGO)
                                    if available or Entrez Gene if not.
7          Ensembl Gene ID      
8          Gene id, Gene symbol     Taken from HUGO, MGD, RGD, ZFIN, TAIR Gene
                                    (as appropriate, dependent on the species).
9          Gene id, Gene symbol     Taken from Entrez Gene.
10         IPI ACs                  All IPI ACs associated with this gene are given.
11         UniProtKB/Swiss-Prot     All UniProtKB/Swiss-Prot ACs associated with
           ACs                      this gene are given.
12         UniProtKB/TrEMBL ACs     All UniProtKB/TrEMBL ACs associated with
                                    this gene are given.
13         Ensembl peptide IDs      All Ensembl peptide IDs associated with this gene
                                    are given. Havana curated transcripts preceeded by
                                    the key HAVANA:
                                    (e.g. ENSP00000341800;HAVANA:ENSP00000317992;).
14         RefSeq STATUS:ID         All RefSeq STATUS:ID couples associated with this
           couples                  gene are given (RefSeq entry revision status details: 
                                    http://www.ncbi.nlm.nih.gov/RefSeq/key.html#status).
15         TAIR Protein IDs         All TAIR Protein IDs associated with this gene
                                    are given.
16         H-InvDB Protein IDs      All H-InvDB Protein IDs associated with this gene
                                    are given.
17         UniGene Gene IDs         All UniGene Gene IDs associated with this gene
                                    are given.
18         CCDS IDs                 All CCDS IDs associated with this gene are given.
19         RefSeq GI protein IDs    All GI protein IDs associated with this gene
                                    are given.
20         Vega Gene ID      
21         Vega peptide IDs         All Vega peptide IDs associated with this gene
                                    are given.

Answer 2

[Ahill]

Where do your ribosomal gene identifers come from (Genbank accessions, UniProt accessions, ...?). As noted by Varun, IPI is deprecated, but if you need IPI IDs for comparison with legacy data, one method is:

1. Go to http://www.uniprot.org
2. Select the ID Mapping Tab
3. Paste or upload your ribosomal gene identifiers
4. Select the type of your source identifiers in the "From" box
5. Select IPI in the "To" box.
6. Click Map. Download the resulting .list file of IPI identifiers

All inter-database identifier mappings should be checked for carefully for accuracy, depending on your application, since determining a "correct" mapping can be complicated.

[Louis]

This no longer works