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Old Swiss-Prot releases

Published November 28, 2003

Swiss-Prot release 42.6 of 28-Nov-2003

New comment line (CC) topic RNA EDITING

We have introduced a new comment (CC) line topic: 'RNA EDITING'. This topic is used to convey information relevant to all types of RNA editing that lead to one or more amino acid changes.

The format of this comment block is:

CC   -!- RNA EDITING: Modified_positions={x[, y, z, ...] | Not_applicable | Undetermined}[; Note=Text].

Examples:

CC   -!- RNA EDITING: Modified_positions=393, 431, 452, 495.
CC   -!- RNA EDITING: Modified_positions=59, 78, 94, 98, 102, 121; Note=The
CC       stop codon at position 121 is created by RNA editing. The nonsense
CC       codon at position 59 is modified to a sense codon.
CC   -!- RNA EDITING: Modified_positions=Not_applicable; Note=Some
CC       positions are modified by RNA editing via nucleotide insertion or
CC       deletion. The initiator methionine is created by RNA editing.

The free text in the 'Note' is standardized.

All entries with such a topic have the keyword RNA editing.

Changes concerning keywords

New keyword:

Swiss-Prot release 42.5 of 21-Nov-2003

Headlines: Monkey business!

The comparison of the genome of human with that of higher apes such as chimpanzees, gibbons, gorillas and the orangutans, was for a long time a wish of many life scientists.

It is becoming a reality due to various sequencing initiatives targeted toward the elucidation of primate genomic sequences. However it will take some time before a significant amount of high quality complete protein sequences are available. In the meanwhile we are trying to ensure that whenever an existing higher ape sequence is available that correspond to a cognate human protein, that sequence gets annotated very quickly.

For example, in the last two weeks, the number of annotated chimpanzees protein sequences in Swiss-Prot has doubled.

Swiss-Prot release 42.4 of 14-Nov-2003

Content changes in the speclist.txt document file

The speclist.txt file lists the organism identification codes which are used to build the "organism" part of an entry name (Examples: ARATH, BACSU, DROME, HUMAN, etc). This file contains for each organism code, the corresponding NCBI taxonomic database node identifier (TaxID) as well as the specific official (scientific) name and optionally common name and synonym.

Up to now organisms identification codes where only used in Swiss-Prot where all species represented in the database are associated with such a code. The TrEMBL section of the combined UniProt knowledgebase will soon also make use of entry names that are based on the species of origin. As it is not possible in a reasonable time frame to manually assign organism codes to all species represented in TrEMBL, it was decided to define "virtual" codes that regroup organisms at a certain taxonomic level. Such codes are prefixed by the number "9" and generally correspond to a "pool" of organisms which can be 'wide' as a kingdom. Here are some examples of such codes:

9BACT B      2: N=Bacteria
9CNID E   6073: N=Cnidaria
9FUNG E   4751: N=Fungi
9REOV V  10880: N=Reoviridae
9TETR E  32523: N=Tetrapoda
9VIRI E  33090: N=Viridiplantae

The list of all the "9" codes that have been defined are now been integrated as a subsection of the speclist.txt file.

Changes concerning the controlled vocabulary for PTMs

New terms for the Feature key 'LIPID':

  • GPI-anchor amidated residue
  • Omega-hydroxyceramide glutamate ester
  • Phosphatidylethanolamine amidated glycine

Changes concerning keywords

New keyword:

Swiss-Prot release 42.3 of 07-Nov-2003

Headlines: More than 10'000 human proteins have been annotated

In the framework of the HPI project, we have annotated more than 10'000 proteins (almost 10'300). The exact number of genes represented is not exactly equal to the number of proteins for at least four reasons:

  • We have entries that describe proteins encoded by more than one gene but whose amino acid sequences are 100% identical;
  • We sometimes are unable to describe highly divergent splice isoforms in one entry and these genes are therefore represented by two or more Swiss-Prot entries;
  • For MHC histocompatibility antigens, immunoglobulin and T cell receptors, we often have several entries representing groups of alleles;
  • A very small number of human entries probably represent "bogus" proteins originating from either pseudogenes or from contaminants.

But even taking the above factors into account, we do have more than 10'000 protein-encoding genes represented in Swiss-Prot.

Cross-references to DictyBase

We have added cross-references to the DictyBase database (available at http://dictybase.org/), an online informatics resource for Dictyostelium discoideum. DictyBase goals are to provide a single portal for access to Dictyostelium genome information, curated Dictyostelium literature, to facilitate access to experimental resources such as the Dictyostelium stock center, and to provide an on-line presence for the Dictyostelium community.

The identifiers of the appropriate DR line are:

Resource abbreviation DictyBase
Resource identifier DictyBase's unique identifier for a gene.
Optional information 1 DictyBase's gene symbol.
Example
P34092:
DR   DictyBase; DDB0002013; myoB.

Cross-refereces to DictyDb

Due to the availability of DictyBase (see above) and in agreement with the maintainers of both databases, we have removed all cross-references to the DictyDb database.

Cross-refereces to PhotoList

We have added cross-references to the PhotoList database (available at http://genolist.pasteur.fr/PhotoList/), a database dedicated to the analysis of the genome of Photorhabdus luminescens strain TT01.

The identifiers of the appropriate DR line are:

Resource abbreviation PhotoList
Resource identifier PhotoList's unique identifier for an ORF.
Example
Q8KM01:
DR   PhotoList; plu1253; -.

Changes concerning keywords

New keyword:

Deleted keywords:

  • B-cell
  • Bone

Swiss-Prot release 42.1 of 24-Oct-2003

Format change in the jourlist.txt document file

The jourlist.txt file lists the titles and abbreviations of all journals cited in Swiss-Prot. This file also includes other type of information such as ISSN and CODEN identifiers, publishers, web sites, etc. As of this release, we have added a field for the ISSN of the electronic (on-line) version of journals. This field which is termed "e-ISSN" is optional.

Example:

Abbrev: Acta Haematol.
Title : Acta Haematologica
ISSN  : 0001-5792
e-ISSN: 1421-9662
CODEN : ACHAAH
Publis: Karger AG
Server: http://www.karger.com/journals/aha/

Changes concerning keywords

New keyword:

Deleted keywords:

  • Alkylation
  • Brain
  • Cartilage

Swiss-Prot release 42.0 of 10-Oct-2003

Headlines: New major release is available (42.0)

Release 42.0 of Swiss-Prot contains 135'850 sequence entries, comprising 50'046'799 amino acids abstracted from 109'694 references. 13'374 sequences have been added since release 41, the sequence data of 1'298 existing entries has been updated and the annotations of 45'617 entries have been revised. This represents an increase of 11%.

Many improvements were carried out in the last 6 months at the level of the CC and FT lines. All the recent changes to Swiss-Prot format are described in detail in the continuously updated document:

Swiss-Prot release 41.26 of 04-Oct-2003

Controlled vocabulary in the feature (FT) key LIPID

We have revised the annotation of post-translational modified amino acids in lipoproteins, and made a major overhaul of the controlled vocabulary. Lipid annotation that was covered by other feature (FT) keys than LIPID has been moved accordingly, e.g. cholesterol-binding.

The currently defined controlled vocabulary for the feature descriptions of 'LIPID' FT lines is listed below:

Cholesterol glycine ester
Cis-14-hydroxy-10,13-dioxo-7-heptadecenoic acid aspartate ester 
GPI-anchor amidated alanine
GPI-anchor amidated asparagine
GPI-anchor amidated aspartate
GPI-anchor amidated cysteine
GPI-anchor amidated glycine
GPI-anchor amidated serine
GPI-anchor amidated threonine
GPI-like-anchor amidated glycine
GPI-like-anchor amidated serine
N-myristoyl glycine
N-palmitoyl cysteine
N(6)-myristoyl lysine
N(6)-palmitoyl lysine
O-octanoyl serine
O-palmitoyl serine
O-palmitoyl threonine
Phosphotidylethanolamine amidated glycine 
S-12-hydroxyfarnesyl cysteine
S-archaeol cysteine
S-diacylglycerol cysteine
S-farnesyl cysteine
S-geranylgeranyl cysteine
S-myristoyl cysteine
S-palmitoleyl cysteine
S-palmitoyl cysteine

Swiss-Prot release 41.24 of 19-Sep-2003

Changes concerning keywords

Deleted keyword:

  • T-DNA

Swiss-Prot release 41.22 of 29-Aug-2003

Changes concerning keywords

Modified keywords:

New keyword:

Swiss-Prot release 41.21 of 22-Aug-2003

Changes concerning keywords

Modified keyword:

New keyword:

Swiss-Prot release 41.20 of 16-Aug-2003

Case and wording change for submissions to Swiss-Prot in reference location (RL) lines

While proceeding with the conversion to mixed case of the different line types of a Swiss-Prot entry, we have decided to do the same for the name of our database, e.g. we are now using "Swiss-Prot" (instead of previously "SWISS-PROT") as the prevalent way of referring to it. This change affects the Swiss-Prot RL (reference location) lines of entries which were submitted directly to Swiss-Prot, and which the authors have not (yet) published. At the same time, we have changed the wording of those lines.

Former format:

RL   Submitted (MAY-2002) to the SWISS-PROT data bank.

New format:

RL   Submitted (MAY-2002) to Swiss-Prot.

Note: RL lines concerning submissions to EMBL/GenBank/DDBJ, PDB and other databases are not affected by this modification.

New comment line (CC) topic ALLERGEN

We have introduced a new comment (CC) line topic type: ALLERGEN. This topic is used to convey information relevant to allergenic proteins.

The format of this comment block is:

CC   -!- ALLERGEN: Text.

Examples:

 P19121: 
CC   -!- ALLERGEN: Causes an allergic reaction in human. Binds IgE. It is a
CC       partially heat-labile allergen that may cause both respiratory and
CC       food-allergy symptoms in patients with the bird-egg syndrome.
 Q28050: 
CC   -!- ALLERGEN: Causes an allergic reaction in human. Minor allergen of
CC       bovine dander.

Swiss-Prot release 41.18 of 25-Jul-2003

Headlines: Annotation of microbial H(+)-translocating pyrophosphatases

We have annotated the microbial H(+)-translocating pyrophosphatases present in the acidocalcisome, the first eukaryotic organelle to be found in bacteria.

Acidocalcisomes are organelles that have an acidic nature, high eletronic density and contain high concentrations of calcium, magnesium, pyrophosphate and polyP. They were originally found in unicellular eukaryotes, such as Toxoplasma gondii and trypanosomatids. It has been postulated that acidocalcisomes may have an important role as an energy source and in the regulation of intracellualr pH, calcium concentration and osmotic conditions.

Now the group of Roberto Docampo has found them in the bacterium Agrobacterium tumefaciens. This is the first organelle to be found in bacteria that have a direct counterpart in eukaryotes. The typical characteristic of the acidocalcisome is the presence of a number of pumps and exchangers: one of them is the H(+)-translocating pyrophosphatase (H+-PPase). This pump generates a proton motive force and may be responsible for the synthesis of pyrophosphate. They are found in several bacteria and archaea and at present it is unkown whether any of these is also localized in acidocalcisomes. As these pumps are present only in some pathogenic bacteria but not in humans, drugs that target them might be effective against these infections.

Changes concerning keywords

Modified keyword:

Swiss-Prot release 41.17 of 19-Jul-2003

Cross-references to GermOnline

We have added cross-references to the GermOnline database (available at http://germonline.unibas.org/), which is maintained by the Genome Bioinformatics group of the SIB Swiss Institute of Bioinformatics. GermOnline is a gateway for gametogenesis. Its goals are to provide a rapid access to a comprehensive compilation of genes, expression data and functions implicated in germline development, meiosis, gamete formation, and gamete function in 11 key model systems and H. sapiens. At this time, the majority of cross-references in Swiss-Prot concern Saccharomyces cerevisiae gene expression data.

The identifiers of the appropriate DR line are:

Resource abbreviation GermOnline
Resource identifier GermOnline's identifier for a gene.
Example
P58012:
DR   GermOnline; 305011; -.

Swiss-Prot release 41.16 of 11-Jul-2003

Changes concerning keywords

New keywords:

Swiss-Prot release 41.14 of 27-Jun-2003

Changes concerning keywords

New keywords:

Swiss-Prot release 41.12 of 16-Jun-2003

New feature key CROSSLNK, and removal of the feature keys THIOETH and THIOLEST

The feature key CROSSLNK has been introduced to describe bonds between amino acids, which are formed posttranslationally within a peptide or between peptides, such as isopeptidic bonds, carbon-carbon linkages, carbon-nitrogen linkages, thioether bonds, thiolester bonds, and backbone condensations.

Format:

FT   CROSSLNK    from     to      Description.       

The initially defined controlled vocabulary is listed below:

1'-histidyl-3'-tyrosine (His-Tyr)
2-cysteinyl-L-phenylalanine (Cys-Phe)
2-cysteinyl-D-phenylalanine (Cys-Phe)
2-cysteinyl-D-allo-threonine (Cys-Thr)
2-iminomethyl-5-imidazolinone (Gln-Gly)
2-oxazoline (Cys-Ser)
2'-(S-cysteinyl)histidine (Cys-His)
3-cysteinyl-aspartic acid (Cys-Asp)
3'-histidyl-3-tyrosine (His-Tyr)
3'-(S-cysteinyl)-tyrosine (Cys-Tyr)
4-cysteinyl-glutamic acid (Cys-Glu)
4'-cysteinyl-tryptophylquinone (Cys-Trp)
5-imidazolinone (Ser-Gly)
5-imidazolinone (Ala-Gly)
5-imidazolinone (Cys-Gly)
Beta-methyllanthionine (Cys-Thr)
Beta-methyllanthionine (Thr-Cys)
Beta-methyllanthionine sulfoxide (Cys-Thr)
Isoaspartyl glycine isopeptide (Asn-Gly)
Isoaspartyl lysine isopeptide (Lys-Asn) (interchain with N-...)
Isoaspartyl lysine isopeptide (Asn-Lys) (interchain with K-...)
Isodityrosine (Tyr-Tyr)
Isoglutamyl cysteine thioester (Gln-Cys)
Isoglutamyl lysine isopeptide (Lys-Gln)
Isoglutamyl lysine isopeptide (Gln-Lys)
Isoglutamyl lysine isopeptide (Gln-Lys) (interchain with K-...)
Isoglutamyl lysine isopeptide (Lys-Gln) (interchain with Q-...)
Lanthionine (Ser-Cys)
Lanthionine (Cys-Ser)
Lysinoalanine (Lys-Ser)
Lysine tyrosylquinone (Lys-Tyr)
Lysinoalanine (Ser-Lys)
Lysyl topaquinone (Lys-Tyr)
N-isoaspartyl cysteine isopeptide (Asn-Cys)
Oxazole (Cys-Ser)
Oxazole (Gly-Ser)
Pyrroloquinoline quinone (Glu-Tyr)
S-(2-aminovinyl)-D-cysteine (Ser-Cys)
S-(2-aminovinyl)-3-methyl-D-cysteine (Thr-Cys)
Thiazole (Gly-Cys)
Thiazole (Ser-Cys)
Thiazole (Phe-Cys)
Thiazole (Cys-Cys)
Thiazole (Lys-Cys)
Tryptophan tryptophylquinone (Trp-Trp)
Glycyl lysine isopeptide (Gly-Lys) (interchain with K-...)
Glycyl lysine isopeptide (Lys-Gly) (interchain with G-...)
Ubiquitinyl cysteine thioester (Cys)

Examples:

 P01024:
FT   CROSSLNK   1010   1013       Isoglutamyl cysteine thioester (Cys-Gln).
 P29827:
FT   CROSSLNK     60     77       Beta-methyllanthionine (Cys-Thr).
FT   CROSSLNK     63     73       Lanthionine (Ser-Cys).
FT   CROSSLNK     64     70       Beta-methyllanthionine (Cys-Thr).
FT   CROSSLNK     65     78       Lysinoalanine (Ser-Lys).

Note: The feature keys THIOETH and THIOLEST have been removed. Various bonds between amino-acids that used to be described by the feature keys BINDING, MOD_RES or SITE will progressively, in groups according the type of PTM, be modified and indicated by CROSSLNK. Disulfide bonds occur so often in proteins, that we decided to keep the special feature key DISULFID to annotate this kind of linkage.

Changes concerning keywords

New keywords:

Swiss-Prot release 41.10 of 30-May-2003

Reference Comment (RC) line topics may span lines

The RC (Reference Comment) line store comments relevant to the reference cited, in currently 5 distinct topics: PLASMID, SPECIES, STRAIN, TISSUE and TRANSPOSON. It is not always possible to list all information within one line. Therefore we allow multiple RC lines, in which one topic might span over a line. Example:

 Q9EVG8:
RC   STRAIN=AZ.026, DC.005, GA.039, GA2181, IL.014, IN.018, KY.172, KY2.37,
RC   LA.013, MN.001, MNb027, MS.040, NY.016, OH.036, TN.173, TN2.38,
RC   UT.002, AL.012, AZ.180, MI.035, VA.015, and IL2.17;

Cross-references to Genome Knowledgebase (GK)

We have added cross-references to the Genome Knowledgebase (GK) (available at http://www.genomeknowledge.org/), which is a collaboration among Cold Spring Harbor Laboratory, The European Bioinformatics Institute, and The Gene Ontology Consortium to develop a curated resource of core pathways and reactions in human biology.

The identifiers of the appropriate DR line are:

Resource abbreviation GK
Resource identifier GK's unique identifier for a protein, which is identical to the Swiss-Prot primary AC number of that protein.
Example
Q9BZJ0:
DR   GK; Q9BZJ0; -.

Cross-references to PIR SuperFamilies of iProClass

We have added cross-references to the PIR SuperFamilies of iProClass (available at http://pir.georgetown.edu/iproclass/), which is an integrated protein classification database.

The identifiers of the appropriate DR line are:

Resource abbreviation PIRSF
Resource identifier iProClass superfamily number.
Optional information 1 Name for a superfamily.
Optional information 2: Number of hits found in the sequence, which is generally '1'.
Example
O28076:
DR   PIRSF; PIRSF006414; FTR; 1.

Swiss-Prot release 41.9 of 24-May-2003

Changes concerning keywords

New keyword:

Swiss-Prot release 41.5 of 23-Apr-2003

Headlines: SARS coronavirus protein sequences are available

We have made a first annotation run of the proteins potentially encoded by the SARS (Severe Acute Respiratory Syndrome) coronavirus. The following entries are available:

Nucleocapsid protein (P59595) E1 glycoprotein (P59596) E2 glycoprotein (P59594 Envelope protein (P59637) Replicase polyprotein 1ab (P59641) Hypothetical protein X1 (P59632) Hypothetical protein X2 (P59633) Hypothetical protein X3 (P59634) Hypothetical protein X4 (P59635) Hypothetical protein 5 (P59636)

Changes concerning keywords

New keywords:

Swiss-Prot release 41.8 of 16-May-2003

Headlines: Complete update of PDB cross-references

We have completely updated our cross-references to PDB. Thanks to work done by the EBI and Geneva Swiss-Prot groups in collaboration with the EBI MSD (Macromolecular Structure Database) group we have mapped at the atom level PDB structural data to the relevant Swiss-Prot and TrEMBL entries. This work has led to the introduction of cross-references to PDB in TrEMBL and a very significant increase in the number of these cross-references in Swiss-Prot. More than 6'000 cross-references were added and the number of Swiss-Prot entries that are linked to PDB is now above 5'300 (versus about 3'600 before this work was carried out).

Swiss-Prot release 41.3 of 04-Apr-2003

Changes concerning keywords

New keywords:

Swiss-Prot release 41.1 of 25-Mar-2003

New syntax of the CC line topic ALTERNATIVE PRODUCTS

In Swiss-Prot release 41.1 (and in the accompanying TrEMBL release), a new format was introduced for "CC ALTERNATIVE PRODUCTS" lines. The new format is more structured than the previous format. Associated with these changes are the introduction of stable identifiers for each named splice isoform in all entries that describe more than one splice isoform; the extension of feature identifiers, previously only used for human VARIANT and certain CARBOHYD features, to VARSPLIC features in entries from all species.

The new format of the CC line topic ALTERNATIVE PRODUCTS is:

CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative promoter;
CC         Comment=Free text;
CC       Event=Alternative splicing; Named isoforms=n;
CC         Comment=Optional free text;
CC       Name=Isoform_1; Synonyms=Synonym_1[, Synonym_n];
CC         IsoId=Isoform_identifier_1[, Isoform_identifer_n]; 
CC         Sequence=Displayed;
CC         Note=Free text;
CC       Name=Isoform_n; Synonyms=Synonym_1[, Synonym_n];
CC         IsoId=Isoform_identifier_1[, Isoform_identifer_n]; 
CC         Sequence=VSP_identifier_1 [, VSP_identifier_n];
CC         Note=Free text;
CC       Event=Alternative initiation;
CC         Comment=Free text;

The qualifiers are described in the table below:

Topic Description
Event Biological process that results in the production of the alternative forms (Alternative promoter, Alternative splicing, Alternative initiation).
Format: Event=controlled vocabulary;
Example: Event=Alternative splicing;
Named isoforms Number of isoforms listed in the topics 'Name' currently only for 'Event=Alternative splicing'.
Format: Named isoforms=number;
Example: Named isoforms=6;
Comment Any comments concerning one or more isoforms; optional for 'Alternative splicing'; in case of 'Alternative promoter' and 'Alternative initiation' there is always a 'Comment' of free text, which includes relevant information on the isoforms.
Format: Comment=free text;
Example: Comment=Experimental confirmation may be lacking for some isoforms;
Name A common name for an isoform used in the literature or assigned by Swiss-Prot; currenty only available for spliced isoforms.
Format: Name=common name;
Example: Name=Alpha;
Synonyms Synonyms for an isoform as used in the literature; optional; currently only available for spliced isoforms.
Format: Synonyms=Synonym_1[, Synonym_n];
Example: Synonyms=B, KL5;
IsoId Unique identifier for an isoform, consisting of the Swiss-Prot accession number, followed by a dash and a number.
Format: IsoId=acc#-isoform_number[, acc#-isoform_number];
Example: IsoId=P05067-1;
Sequence Information on the isoform sequence; the term Displayed indicates, that the sequence is shown in the entry; a list of feature identifiers (VSP_#) indicates that the isoform is annotated in the feature table; the FTIds enable programs to create the sequence of a splice variant; if the accession number of the IsoId does not correspond to the accession number of the current entry, this topic contains the term External; Not described points out that the sequence of the isoform is unknown.
Format: Sequence=VSP_#[, VSP_#]|Displayed|External|Not described;
Example: Sequence=Displayed;
Example: Sequence=VSP_000013, VSP_000014; Example: Sequence=External;
Example: Sequence=Not described;
Note Lists isoform-specific information; optional.
Format: Note=Free text;
Example: Note=No experimental confirmation available;

Example of the CC lines and the corresponding FT lines for an entry with alternative splicing Q15746:

...
CC  -!- ALTERNATIVE PRODUCTS:
CC      Event=Alternative splicing; Named isoforms=6;
CC      Name=1;
CC        IsoId=Q15746-4; Sequence=Displayed;
CC      Name=2;
CC        IsoId=Q15746-5; Sequence=VSP_000040;
CC      Name=3A;
CC        IsoId=Q15746-6; Sequence=VSP_000041, VSP_000043; 
CC      Name=3B;
CC        IsoId=Q15746-7; Sequence=VSP_000040, VSP_000041, VSP_000042;
CC      Name=4;
CC        IsoId=Q15746-8; Sequence=VSP_000041, VSP_000042;
CC      Name=del-1790;
CC        IsoId=Q15746-9; Sequence=VSP_000044;
...
FT   VARSPLIC    437    506       VSGIPKPEVAWFLEGTPVRRQEGSIEVYEDAGSHYLCLLKA
FT                                RTRDSGTYSCTASNAQGQVSCSWTLQVER -> G (in
FT                                isoform 2 and isoform 3B).
FT                                /FTId=VSP_004791.
FT   VARSPLIC   1433   1439       DEVEVSD -> MKWRCQT (in isoform 3A,
FT                                isoform 3B and isoform 4).
FT                                /FTId=VSP_004792.
FT   VARSPLIC   1473   1545       Missing (in isoform 4).
FT                                /FTId=VSP_004793.
FT   VARSPLIC   1655   1705       Missing (in isoform 3A and isoform 3B).
FT                                /FTId=VSP_004794.
FT   VARSPLIC   1790   1790       Missing (in isoform Del-1790).
FT                                /FTId=VSP_004795.
 
...

The corresponding modules of the Swiss-Prot parser Swissknife have been modified, and Release 1.31 of Swissknife can be downloaded.

Cross-references to Gene Ontology (GO)

We have added cross-references to the Gene Ontology (GO) database (available at http://www.geneontology.org/), which provides controlled vocabularies for the description of the molecular function, biological process and cellular component of gene products.

The identifiers of the appropriate DR line are:

Resource abbreviation GO
Resource identifier GO's unique identifier for a GO term.
Optional information 1 A 1-letter abbreviation for one of the 3 ontology aspects, separated from the GO term by a column. If the term is longer than 46 characters, the first 43 characters are indicated followed by 3 dots ('...'). The abbreviations for the 3 distinct aspects of the ontology are P (biological Process), F (molecular Function), and C (cellular Component).
Optional information 2 3-character GO evidence code. The meaning of the evidence codes is: IDA=inferred from direct assay, IMP=inferred from mutant phenotype, IGI=inferred from genetic interaction, IPI=inferred from physical interaction, IEP=inferred from expression pattern, TAS=traceable author statement, NAS=non-traceable author statement, IC=inferred by curator, ISS=inferred from sequence or structural similarity.
Examples
Q9XTD2
DR   GO; GO:0008601; F:protein phosphatase type 2A, regulator acti...; IPI.
DR   GO; GO:0000080; P:G1 phase of mitotic cell cycle; IDA.
DR   GO; GO:0008285; P:negative regulation of cell proliferation; IDA.
DR   GO; GO:0006470; P:protein amino acid dephosphorylation; IDA.

P04406:
DR   GO; GO:0005737; C:cytoplasm; NAS.
DR   GO; GO:0004365; F:glyceraldehyde 3-phosphate dehydrogenase (p...; NAS.
DR   GO; GO:0006096; P:glycolysis; NAS.

Changes concerning keywords

New keywords:

Deleted keyword:

  • Amphibian skin

Swiss-Prot release 41.0, 28-Feb-2003

Progress in the conversion of Swiss-Prot to mixed-case characters

We are gradually converting Swiss-Prot entries from all UPPER CASE to MiXeD CaSe. With this release the RC (Reference Comment) line topic STRAIN and the CC line topic CATALYTIC ACTIVITY have been converted.

"Nucleomorph" added to the OrGanelle (OG) line

The OG (OrGanelle) line indicates from which genome a gene for a protein originates. Until now, defined terms in the OG line where "Chloroplast", "Cyanelle", "Mitochondrion" and "Plasmid". The term "Nucleomorph" has been added, which is the residual nucleus of an algal endosymbiont that resides inside its host cell.

Multiple RP lines

Starting with release 41, there can be more than one RP (Reference Position) line per reference in a Swiss-Prot entry. The RP line describes the extent of the work carried out by the authors of the reference, e.g. the type of molecule that has been sequenced, protein characterization, PTM characterization, protein structure analysis, variation detection, etc.

As the number of experimental results per publication has increased over the years, the limitation of using a single RP line per reference no longer allowed to add all the information while maintaining a consistent format. Therefore we decided to permit multiple RP lines.

Example:

RP   SEQUENCE FROM N.A., SEQUENCE OF 23-42 AND 351-365, AND
RP   CHARACTERIZATION.

Cross-references to Schizosaccharomyces pombe GeneDB Prototype

We have added cross-references to the Schizosaccharomyces pombe GeneDB Prototype (available at http://www.genedb.org/genedb/pombe/index.jsp), which contains all S. pombe known and predicted protein coding genes, pseudogenes and tRNAs. It is hosted by the Sanger Institute.

The identifiers of the appropriate DR line are:

Resource abbreviation GeneDB_SPombe
Resource identifier GeneDB's unique identifier for a S. pombe gene.
Example
DR   GeneDB_SPombe; SPAC9E9.12c; -.

Cross-referecences to Genew

We have added cross-references to the Human Gene Nomenclature Database Genew (available at http://www.gene.ucl.ac.uk/cgi-bin/nomenclature/searchgenes.pl), which provides data for all human genes which have approved symbols. It is managed by the HUGO Gene Nomenclature Committee (HGNC).

The identifiers of the appropriate DR line are:

Resource abbreviation Genew
Resource identifier HGNC's unique identifier for a human gene
Optional information 1 HGNC's approved gene symbol.
Example
DR   Genew; HGNC:5217; HSD3B1.

Cross-references to Gramene

We have added cross-references to the Gramene database, a comparative mapping resource for grains (available at http://www.gramene.org/).

The format of the explicit links in the flat file is:

Resource abbreviation Gramene
Resource identifier Unique identifier for a protein, which is identical to the Swiss-Prot primary AC number of that protein.
Example
DR   Gramene; Q06967; -.

Cross-references to HAMAP

We have added cross-references to the collection of orthologous microbial protein families, generated manually by expert curators of the HAMAP (High-quality Automated and Manual Annotation of microbial Proteomes) project in the framework of the Swiss-Prot protein knowledgebase. The data is accessible at /sprot/hamap/families.html.

The identifiers of the appropriate DR line are:

Resource abbreviation HAMAP
Resource identifier HAMAP unique identifier for a microbe protein family
Optional information 1 The values are either '-', 'fused', 'atypical' or 'atypical/fused'. The value '-' is a placeholder for an empty field; the 'fused' value indicates that the family rule does not cover the entire protein; the value 'atypical' points out that the protein is divergent in sequence or has mutated functional sites, and should not be included in family datasets. The value 'atypical/fused' indicates both latter findings.
Optional information 2 Number of domains found in the protein, generally '1', rarely '2' for the fusion of 2 identical domains.
Example
DR   HAMAP; MF_00012; -; 1.

Cross-references to Phosphorylation Site Database

We have added cross-references to the Phosphorylation Site Database, PhosSite (available at http://vigen.biochem.vt.edu/xpd/xpd.htm), which provides access to information from scientific literature concerning prokaryotic proteins that undergo covalent phosphorylation on the hydroxyl side chains of serine, threonine or tyrosine residues.

The identifiers of the appropriate DR line are:

Resource abbreviation PhosSite
Resource identifier Unique identifier for a phosphoprotein, which is identical to the Swiss-Prot primary AC number of that protein.
Example
DR   PhosSite; P00955; -.

Cross-references to TIGRFAMs

We have added cross-references to TIGRFAMs, a protein family database available at http://www.tigr.org/TIGRFAMs/.

The identifiers of the appropriate DR line are:

Resource abbreviation TIGRFAMs
Resource identifier TIGRFAMs' unique identifier for a protein family.
Optional information 1 TIGRFAMs' entry name for a protein family.
Optional information 2 Number of hits found in the sequence.
Example
DR   TIGRFAMs; TIGR00630; uvra; 1.

Cross-references to CarbBank

We have removed the Swiss-Prot cross-references to CarbBank.

Cross-references to GCRDb

We have removed the Swiss-Prot cross-references to GCRDb.

Cross-references to Mendel

We have removed the Swiss-Prot cross-references to Mendel.

Cross-references to YEPD

We have removed the Swiss-Prot cross-references to the yeast electrophoresis protein database (YEPD).

Explicit links to dbSNP in FT VARIANT lines of human sequence entries

In human protein sequence entries we have introduced explicit links to the Single Nucleotide Polymorphism database (dbSNP) from the feature description of FT VARIANT keys.

The format of such links is:

FT   VARIANT    from     to	  description (IN dbSNP:accession_number).
FT                                /FTId=VAR_number.
Example:
FT   VARIANT      65     65       T -> I (IN dbSNP:1065419).
FT                                /FTId=VAR_012009.

Feature key SIMILAR became obsolete

The feature key SIMILAR was used to describe the extent of a similarity with another protein sequence. Nowadays, most domains with similarity to other proteins are known regions described in domain and family databases, which are annotated in Swiss-Prot with the feature key DOMAIN or REPEAT and the comment (CC) line topic SIMILARITY; thus the feature key SIMILAR became obsolete and will not be used again.

Version of SP in XML format

A distribution version of Swiss-Prot and TrEMBL in XML format is being developed. The first draft of the XML specification was released for public review on February 21, 2002.