General context
We are introducing evidence tags to parts of UniProt Knowledgebase entries. These tags will allow
1. UniProt staff and users to see where data items came from
2. UniProt staff to automatically update data if the underlying evidence
changes
Data items to tag
All relevant data items of an entry will ultimately have one or more evidence
tags. A data item may be a single word, e.g. a keyword, or an object extending
over multiple lines, e.g. a comment in the CC line.
Evidence tagging logic
Each data item may have one or more evidence tags. Each tag refers to
one piece of evidence that supports the data item. Therefore, if one
piece of evidence becomes invalid, e.g. through a change to a rule for
automatic annotation, the data item will be deleted if the deleted
evidence tag was the last one supporting the data item. This allows us
to automatically keep data added by automatic annotation procedures
up-to-date.
Contents of an evidence tag
Each evidence tag consists of four elements:
1. Category
Evidence types are grouped into three major categories:
 curator = Manual curation
import = Import from other data sources
program = A program has added/created information
2. Type
For examples of evidence types see the table below
for the list of evidence types.
3. Attributes
If several attributes are needed to completely describe the
data source, they will be concatenated with commas.
4. Date
The date of the last update of the data item.
|
Type
|
Category
|
Type description
|
Attribute
|
Example
|
|
EMBL
|
import
|
Information copied from the EMBL/GenBank/DDBJ entry
|
proteinID.version
|
<evidence category="import" type="EMBL" attribute="BAA82799.1" date="2001-09-30" evID="EI2" />
|
|
TrEMBL
|
program
|
Information from the EMBL/GenBank/DDBJ entry, modified during the
creation of the TrEMBL entry to correct errors or to comply with Swiss-Prot syntax.
|
EMBL proteinID.version
|
<evidence category="program" type="TrEMBL" attribute="CAA09143.1" date="2001-09-30" evID="EP3" />
|
|
Curator
|
curator
|
Curator judgement
|
none
|
<evidence category="curator" type="Curator" date="2001-11-21" evID="EC1" />
|
|
Similarity
|
curator
|
By similarity to another entry, according to curator judgement.
|
AC of source entry
|
<evidence category="curator" type="Similarity" attribute="P80511" date="2001-12-07" evID="EC4" />
|
|
Experimental
|
curator
|
Experimental evidence, as derived from a reference. The reference will
usually be a paper, but might also be a submission in the case of a direct
submission to Swiss-Prot.
|
Identifier of the reference (if possible the PubMed identifier) in
the form PubMed=10543405. If no PubMed identifier is available, e.g. for
books, the attribute may be omitted.
|
<evidence category="curator" type="Experimental" attribute="PubMed=10993897" date="2001-06-25" evID="EC1" />
<evidence category="curator" type="Experimental" date="2001-06-19" evID="EC2" />
|
|
Opinion
|
curator
|
Opinion stated by the author of a reference, normally with little
or no experimental confirmation.
|
Identifier of reference.
|
<evidence category="curator" type="Opinion" attribute="PubMed=11522286" date="2001-12-06" evID="EC3" />
|
|
Foreign database name
|
import
|
Information derived from foreign databases
by a curator
,
e.g. gene names from MGD.
|
Primary key for the foreign database (AC number)
|
<evidence category="import" type="FLYBASE_ADD" attribute="FBgn0031157" date="2002-08-20" evID="EI1" />
|
|
Rulebase
|
program
|
Information derived from a rulebase rule. Rulebase is the knowledge
base which is used by the TrEMBL automated annotation.
|
Rule number.version
|
<evidence category="program" type="Rulebase" attribute="RU000305V1.82" date="2002-09-17" evID="EA1" />
|
|
SignalP
|
program
|
Information added using the SignalP program.
|
Version number of program and whether organism is eukaryotic, Gram-positive or Gram-negative
|
<evidence category="program" type="SignalP" attribute="V2.0.b2-HMM, eukaryotic" date="2001-05-29" evID="EP3" />
|
|
Other programs
|
program
|
Program name
|
Program version, parameters
|
|
2002-2003, EMBL Outstation - EBI
Current Status
|
