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        SIB Swiss Institute of Bioinformatics; Geneva, Switzerland
        European Bioinformatics Institute (EBI); Hinxton, United Kingdom
        Protein Information Resource (PIR); Washington DC, USA
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Description: Criteria used to assign the PE level of entries
Name:        pe_criteria.txt
Release:     2013_06 of 29-May-2013

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This document lists the criteria used to assign a PE level to entries.


Criteria used to implement the 'PE 1: Evidence at protein level'
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We add the 'Evidence at protein level' qualifier to all entries with at
least one of the annotations listed below:

1. RP lines containing:

   CHARACTERIZATION
   AMINO-ACID COMPOSITION
   CATALYTIC ACTIVITY
   FUNCTION AS, FUNCTION IN
   INTERACTION WITH, SUBUNIT, IDENTIFICATION IN ... COMPLEX
   -BINDING
   IDENTIFICATION BY MASS SPECTROMETRY, MASS SPECTROMETRY
   CRYSTALLIZATION, X-RAY CRYSTALLOGRAPHY, ELECTRON MICROSCOPY, STRUCTURE BY NMR
   CLEAVAGE, PROTEOLYTIC PROCESSING
   TOPOLOGY
   DISULFIDE
   LEVEL OF PROTEIN EXPRESSION
   PTM information (acetylation, glycosylation, methylation,
     phosphorylation, ubiquitination etc.)

2. CC topics:

   ALLERGEN - without the 'By similarity' qualifier
   BIOPHYSICOCHEMICAL PROPERTIES
   BIOTECHNOLOGY
   DEVELOPMENTAL STAGE - with the 'at protein level' qualifier
   INDUCTION - with the 'at protein level' qualifier
   INTERACTION
   MASS SPECTROMETRY
   PHARMACEUTICAL
   TISSUE SPECIFICITY - with the 'at protein level' qualifier
   WEB RESOURCE: NAME=GeneReviews;

3. DR lines:

   COMPLUYEAST-2DPAGE
   UCD-2DPAGE
   SWISS-2DPAGE
   World-2DPAGE
   HPA; CABxxxx
   PeptideAtlas
   ProMEX
   PDB - with the exception of the 'model' category

4. Keywords:

   Direct protein sequencing
   Disease mutation

5. FT lines:

   CARBOHYD - without qualifiers 'By similarity', 'Potential', 'Probable'
   CROSSLNK - without qualifiers 'By similarity', 'Potential', 'Probable'
   DISULFID - without qualifiers 'By similarity', 'Potential', 'Probable'
   LIPID - without qualifiers 'By similarity', 'Potential', 'Probable'
   MOD_RES - without qualifiers 'By similarity', 'Potential', 'Probable'
   MUTAGEN

6. In vivo subcellular location analysis from PubMed=14562095 in
   S.cerevisiae

The 'PE 1' assignment overrides assignment to PE categories 2 to 3.


Criteria used to implement the 'PE 2: Evidence at transcript level'
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We add the 'Evidence at transcript level' qualifier to all entries with at
least one of the annotations listed below:

1. RP lines containing:

   The [MRNA] 'molecule type' [*]
   DEVELOPMENTAL STAGE
   INDUCTION
   RNA EDIT - for non-viral entries only
   TISSUE SPECIFICITY

2. CC topics:

   RNA EDITING - for non-viral entries only and without the qualifiers
   'By similarity' and 'Potential'

3. DR lines:

   ArrayExpress
   CleanEx
   EMBL - with molecule type "mRNA" [*]

[*] These two criteria are only applied to proteins at least 120 residues
    long, since small CDS may be regulatory RNAs that are not translated,
    and to entries of less than 120 residues which are fragments.

The 'PE 2' assignment overrides assignement to PE category 3.


Criteria used to implement the 'PE 3: Inferred from homology'
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We add the 'Evidence from homology' qualifier to all entries with at least
one of the annotations listed below:

"Entries that have a CC SIMILARITY topic with 'Belongs to... *family'."
   Entries that have any CC topic with the 'By similarity' qualifier
   DR lines: HAMAP
   FT lines: SIGNAL, INIT_MET, MOD_RES, LIPID, CROSSLNK with the
   'By similarity' qualifier


Criteria used to implement the 'PE 4: Predicted'
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All entries that are not assigned to categories 1; 2; 3 or 5.


Criteria used to implement the 'PE 5: Uncertain'
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All entries that contain one of the following texts in a CC CAUTION topic:

   'Could be the product of a pseudogene.'
   'Product of a dubious CDS prediction.'
   'Product of a dubious gene prediction.'

The 'PE 5' assignment overrides assignement to PE categories 1, 2 or 3.

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