README iRefIndex Feedback 1.1
Last edited: October 13th, 2008
Applies to iRefIndex release: 1.1 beta.
Release date: July 11th, 2008
Authors: Ian Donaldson and Sabry Razick
Database: iRefIndex (http://irefindex.uio.no)
Organization: Biotechnology Centre of Oslo, University of Oslo (http://www.biotek.uio.no/)
Contents
- 1 Description
- 2 Directory contents
- 3 Changes from last version
- 4 Known Issues
- 5 License
- 6 Citation
- 7 Disclaimer
- 8 Understanding the Feedback file
- 9 Description of Feedback file
- 9.1 Column number: 1
- 9.2 Column number: 2
- 9.3 Column number: 3
- 9.4 Column number: 4
- 9.5 Column number: 5
- 9.6 Column number: 6
- 9.7 Column number: 7
- 9.8 Column number: 8
- 9.9 Column number: 9
- 9.10 Column number: 10
- 9.11 Column number: 11
- 9.12 Column number: 12
- 9.13 Column number: 13
- 9.14 Column number: 14
- 10 Not found file
Description
This file describes the contents of the xxx/feedback directory and the format of the tab-delimited text files contained within.
Directory contents
README this file xxxx.feedback.y.y.txt.zip feedback for some database (xxxx) for release y.y
Changes from last version
None. First release of this file.
Known Issues
None.
License
This directory is private and only released to invited source databases. These data are released under the Creative Commons Attribution License http://creativecommons.org/licenses/by/2.5/. This means that you are free to use, modify and redistribute these data for personal or commercial use so long as you provide appropriate credit. See next section.
Copyright © 2008 Ian Donaldson
Citation
Razick, S., Magklaras, G., Donaldson, IM. iRefIndex: A consolidated protein interaction database with provenance. BMC Bioinformatics. 2008. 9(1):405. PMID 18823568.
Disclaimer
Data is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Understanding the Feedback file
Insert explanatory text here
Description of Feedback file
Each line in this file represents
- a protein interactor found in some source db record and
- the iRefIndex mapping to a current protein sequence record.
Column number: 1
| Column name: | int_acc |
| Column type: | string |
| Description: | accession for interaction record |
| Example: | intact |
Notes
Column number: 2
| Column name: | int_db |
| Column type: | string |
| Description: | name of interaction db |
| Example: | intact |
Notes Possible values in this field are:
| bind | biomolecular interaction network db |
| biogrid | the biogrid db |
| dip | db of interacting proteins |
| hprd | human protein reference db |
| intact | ebi interaction db |
| mint | molecular interaction db |
| mpact | mips yeast protein interaction db |
| mppi | mips mammalian protein interaction db |
| ophid | online predicted human interaction db |
Column number: 3
| Column name: | primary_acc |
| Column type: | string |
| Description: | An accession for a protein interactor in some database as supplied in the interaction record (see columns 1-2) |
| Example: | Q9Y6Q9 |
Notes
Column number: 4
| Column name: | primary_db |
| Column type: | string |
| Description: | source db for accession listed in column 4 |
| Example: | uniprotkb |
Notes
This is the primary protein sequence database referenced in the interaction record.
Column number: 5
| Column name: | primary_taxid |
| Column type: | integer |
| Description: | taxonomy of protein interactor as listed in the source interaction record |
| Example: | 9606 |
Notes
Column number: 6
| Column name: | used_acc |
| Column type: | string |
| Description: | An accession for a protein interactor in some database as supplied in the interaction record (see columns 1-2) |
| Example: | Q9Y6Q9 |
Notes
Column number: 7
| Column name: | used_db |
| Column type: | string |
| Description: | source db for accession listed in column 4 |
| Example: | uniprotkb |
Notes
This is the primary protein sequence database referenced in the interaction record.
Column number: 8
| Column name: | used_taxid |
| Column type: | integer |
| Description: | taxonomy of protein interactor as listed in the source interaction record |
| Example: | 9606 |
Notes
Column number: 9
| Column name: | mapped_acc |
| Column type: | string |
| Description: | the accession that this interactor was mapped to by iRefIndex |
| Example: | Q9Y6Q9 |
Notes This will most likely be the same accession as listed in column 4 unless:
| reason | example | see scores with... |
| a modified version of the accession has been used | NP_0001 in place of NP 0001 | M |
| an updated version of the accession has been used | xxx in place of xxx | U or E |
Column number: 10
| Column name: | mapped_db |
| Column type: | string |
| Description: | the source protein db that this interactor was mapped to by iRefIndex |
| Example: | uniprot |
Notes
This will most likely be the same as the db listed in column 6 unless:
| reason | example | see scores with... |
| the db name is not valid or is a variation of a cv db | uniprot in place of "protein database" | D |
Column number: 11
| Column name: | mapped_taxid |
| Column type: | integer |
| Description: | Taxonomy identifier for interactor as found in source protein db for record specified in column 8 and 9. |
| Example: | 9606 |
Notes
This will most likely be the same as the taxid listed in column 7 unless:
| reason | example | see scores with... |
| the listed taxid is different from that found in the mapped record | xxx in place of xxx | T |
Column number: 12
| Column name: | rogid |
| Column type: | string |
| Description: | rogid of the interactor assigned by iRefIndex |
| Example: | HWcRyNPgZ0dLD9cb5iuiarsGG8E9606 |
Notes See iRefIndex paper. PMID 18823568.
Column number: 13
| Column name: | rogscore |
| Column type: | string |
| Description: | description of assignment score for this interactor |
| Example: | PUTO+ |
Notes
See iRefIndex paper. PMID 18823568.
Column number: 14
| Column name: | score_type |
| Column type: | integer |
| Description: | assignment score type 1-6 |
| Example: | 1 |
Notes
See iRefIndex paper. PMID 18823568. Table 4 column 1
Not found file
Each row in this table represents an interactor reference which we were unable to map to a sequence.
Column number: 1
| Column name: | int_acc |
| Column type: | string |
| Description: | accession for interaction record |
| Example: | intact |
Notes
Column number: 2
| Column name: | int_db |
| Column type: | string |
| Description: | name of interaction db |
| Example: | intact |
Notes Possible values in this field are:
| bind | biomolecular interaction network db |
| biogrid | the biogrid db |
| dip | db of interacting proteins |
| hprd | human protein reference db |
| intact | ebi interaction db |
| mint | molecular interaction db |
| mpact | mips yeast protein interaction db |
| mppi | mips mammalian protein interaction db |
| ophid | online predicted human interaction db |
Column number: 3
| Column name: | unfound_acc |
| Column type: | string |
| Description: | An accession for a protein interactor in some database as supplied in the interaction record (see columns 1-2) |
| Example: | Q9Y6Q9 |
Notes
Column number: 4
| Column name: | unfound_db |
| Column type: | string |
| Description: | source db for accession listed in column 4 |
| Example: | uniprotkb |
Notes
This is the primary protein sequence database referenced in the interaction record.
Column number: 5
| Column name: | unfound_taxid |
| Column type: | integer |
| Description: | taxonomy of protein interactor as listed in the source interaction record |
| Example: | 9606 |
Notes
