Difference between revisions of "README iRefIndex Feedback 1.1"

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# a protein interactor found in some source db record and  
 
# a protein interactor found in some source db record and  
 
# the iRefIndex mapping to a current protein sequence record.  
 
# the iRefIndex mapping to a current protein sequence record.  
−
 
  
 
=== Column number: 1 ===
 
=== Column number: 1 ===
  
 
{|
 
{|
−
|Column name: ||sourcedb
+
|Column name: ||int_acc
 
|-
 
|-
 
|Column type: ||string
 
|Column type: ||string
 
|-
 
|-
−
|Description: ||name of interaction db
+
|Description: ||accession for interaction record
 
|-
 
|-
 
|Example: || intact
 
|Example: || intact
Line 78: Line 77:
  
 
{|
 
{|
−
|Column name: ||sourceacc
+
|Column name: ||int_db
 
|-
 
|-
 
|Column type: ||string
 
|Column type: ||string
 
|-
 
|-
−
|Description: ||accession of interaction record in the source
+
|Description: ||name of interaction db
 
|-
 
|-
−
|Example: ||??? some accession in intact
+
|Example: || intact
 
|}
 
|}
  
 
'''Notes'''
 
'''Notes'''
 +
Possible values in this field are:
 +
{||class="wikitable" style="text-align:left" border="1" cellpadding="5"
 +
| 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 number: 3 ===
  
 
{|
 
{|
−
|Column name: ||uid
+
|Column name: ||primary_acc
 
|-
 
|-
−
|Column type: ||integer
+
|Column type: ||string
 
|-
 
|-
−
|Description: ||the iRefIndex integer identifier for this interactor in this release
+
|Description: ||An accession for a protein interactor in some database as supplied in the interaction record (see columns 1-2)
 
|-
 
|-
−
|Example: ||1958262
+
|Example: ||Q9Y6Q9
 
|}
 
|}
  
 
'''Notes'''
 
'''Notes'''
  
−
This is an internal integer identifier and may change from one release of iRefIndex to another.
 
  
 
=== Column number: 4 ===
 
=== Column number: 4 ===
  
 
{|
 
{|
−
|Column name: ||acc
+
|Column name: ||primary_db
 
|-
 
|-
 
|Column type: ||string
 
|Column type: ||string
 
|-
 
|-
−
|Description: ||An accession for a protein interactor in some database as supplied in the interaction record (see columns 1-2)
+
|Description: ||source db for accession listed in column 4
 
|-
 
|-
−
|Example: ||Q9Y6Q9
+
|Example: ||uniprotkb
 
|}
 
|}
  
 
'''Notes'''
 
'''Notes'''
  
−
 
+
This is the primary protein sequence database referenced in the interaction record.
  
 
=== Column number: 5 ===
 
=== Column number: 5 ===
  
 
{|
 
{|
−
|Column name: ||category
+
|Column name: ||primary_taxid
 
|-
 
|-
 
|Column type: ||integer
 
|Column type: ||integer
 
|-
 
|-
−
|Description: ||Type of accession provided in column 4
+
|Description: ||taxonomy of protein interactor as listed in the source interaction record
 
|-
 
|-
−
|Example: ||2
+
|Example: ||9606
 
|}
 
|}
  
 
'''Notes'''
 
'''Notes'''
  
−
Possible vaules are:
+
 
−
{||class="wikitable" style="text-align:left" border="1" cellpadding="5"
+
=== Column number: 6 ===
−
| 2 ||Primary reference for interactor supplied in interaction record
+
 
 +
{|
 +
|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)
 
|-
 
|-
−
| 3 ||Secondary reference for interactor supplied in interaction record
+
|Example: ||Q9Y6Q9
 
|}
 
|}
  
−
=== Column number: 6 ===
+
'''Notes'''
 +
 
 +
 
 +
=== Column number: 7 ===
  
 
{|
 
{|
−
|Column name: ||source
+
|Column name: ||used_db
 
|-
 
|-
 
|Column type: ||string
 
|Column type: ||string
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This is the primary protein sequence database referenced in the interaction record.
 
This is the primary protein sequence database referenced in the interaction record.
  
−
 
+
=== Column number: 8 ===
−
 
 
−
=== Column number: 7 ===
 
  
 
{|
 
{|
−
|Column name: ||taxid
+
|Column name: ||used_taxid
 
|-
 
|-
 
|Column type: ||integer
 
|Column type: ||integer
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'''Notes'''
 
'''Notes'''
  
−
 
+
=== Column number: 9 ===
−
=== Column number: 8 ===
 
  
 
{|
 
{|
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|}
 
|}
  
−
=== Column number: 9 ===
+
=== Column number: 10 ===
  
 
{|
 
{|
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This will most likely be the same as the db listed in column 6 unless:
 
This will most likely be the same as the db listed in column 6 unless:
−
{|
+
{||class="wikitable" style="text-align:left" border="1" cellpadding="5"
 
|reason||example||see scores with...
 
|reason||example||see scores with...
 
|-
 
|-
Line 218: Line 243:
 
|}
 
|}
  
−
=== Column number: 10 ===
+
=== Column number: 11 ===
  
 
{|
 
{|
−
|Column name: ||mapped_tax
+
|Column name: ||mapped_taxid
 
|-
 
|-
 
|Column type: ||integer
 
|Column type: ||integer
Line 233: Line 258:
  
 
This will most likely be the same as the taxid listed in column 7 unless:
 
This will most likely be the same as the taxid listed in column 7 unless:
−
{|
+
{||class="wikitable" style="text-align:left" border="1" cellpadding="5"
 
|reason||example||see scores with...
 
|reason||example||see scores with...
 
|-
 
|-
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|}
 
|}
  
−
=== Column number: 11 ===
+
=== Column number: 12 ===
  
 
{|
 
{|
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See iRefIndex paper. PMID 18823568.  
 
See iRefIndex paper. PMID 18823568.  
  
−
=== Column number: 12 ===
+
=== Column number: 13 ===
  
 
{|
 
{|
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See iRefIndex paper. PMID 18823568.  
 
See iRefIndex paper. PMID 18823568.  
  
−
=== Column number: 13 ===
+
=== Column number: 14 ===
  
 
{|
 
{|
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See iRefIndex paper. PMID 18823568. Table 4 column 1
 
See iRefIndex paper. PMID 18823568. Table 4 column 1
  
−
=== Column number: 14 ===
+
 
 +
 
 +
== 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:
 +
{||class="wikitable" style="text-align:left" border="1" cellpadding="5"
 +
| 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: ||rog
+
|Column name: ||unfound_acc
 
|-
 
|-
−
|Column type: ||integer
+
|Column type: ||string
 
|-
 
|-
−
|Description: ||an internal integer equivalent of column 11
+
|Description: ||An accession for a protein interactor in some database as supplied in the interaction record (see columns 1-2)
 
|-
 
|-
−
|Example: ||2296393
+
|Example: ||Q9Y6Q9
 
|}
 
|}
  
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 +
=== Column number: 4 ===
  
−
=== Column number: 15 ===
+
{|
 +
|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: ||refrog
+
|Column name: ||unfound_taxid
 
|-
 
|-
 
|Column type: ||integer
 
|Column type: ||integer
 
|-
 
|-
−
|Description: ||explain xxx ???
+
|Description: ||taxonomy of protein interactor as listed in the source interaction record
 
|-
 
|-
−
|Example: || 2296393
+
|Example: ||9606
 
|}
 
|}
  
 
'''Notes'''
 
'''Notes'''
  
−
explain xxx ???
+
[[Category:iRefIndex]]

Latest revision as of 17:29, 4 March 2009

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/)

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

  1. a protein interactor found in some source db record and
  2. 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

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