Migration Guide

UniProt

The original flat text format is described in the UniProt user manual.

ID/AC - Header

ID   CASA1_SHEEP             Reviewed;         214 AA.
AC   P04653; Q69B23; Q9TS03; Q9TS48;

uniprot:P04653
  reviewed true
  mnemonic "CASA1_SHEEP"
  replaces uniprot:Q69B23
  replaces uniprot:Q9TS03
  replaces uniprot:Q9TS48

Changes:

• The role of different identifiers is made explicit. Note that while CASA1_SHEEP can be used to refer to an entry it is not a stable identifier.
• The Reviewed and Unreviewed markers are replaced by a boolean value that indicates whether an entry was reviewed or not.

DT - Dates

DT   01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT   01-NOV-1996, sequence version 1.
DT   16-DEC-2008, entry version 93.

uniprot:Q15848
  created 1997-11-01
  modified 2008-12-16
  version 93
  sequence <http://purl.uniprot.org/isoforms/Q15848-1>
    rdf:type Simple_Sequence
    modified 1996-11-01
    version 1

Changes:

• Made use of international standard date notation.
• Moved the sequence version and the date of the last sequence modification to the sequence.

DE - Description

DE   RecName: Full=Arginine biosynthesis bifunctional protein argJ;
DE   Includes:
DE     RecName: Full=Glutamate N-acetyltransferase;
DE              EC=2.3.1.35;
DE     AltName: Full=Ornithine acetyltransferase;
DE              Short=OATase;
DE     AltName: Full=Ornithine transacetylase;
DE   Includes:
DE     RecName: Full=Amino-acid acetyltransferase;
DE              EC=2.3.1.1;
DE     AltName: Full=N-acetylglutamate synthase;
DE              Short=AGS;
DE   Contains:
DE     RecName: Full=Arginine biosynthesis bifunctional protein argJ alpha chain;
DE   Contains:
DE     RecName: Full=Arginine biosynthesis bifunctional protein argJ beta chain;

uniprot:Q07908
  recommendedName 
    rdf:type Structured_Name
    fullName "Arginine biosynthesis bifunctional protein argJ"
  component 
    rdf:type Part
    recommendedName 
      rdf:type Structured_Name
      fullName "Arginine biosynthesis bifunctional protein argJ alpha chain"
  component 
    rdf:type Part
    recommendedName 
      rdf:type Structured_Name
      fullName "Arginine biosynthesis bifunctional protein argJ beta chain"
  domain 
    rdf:type Part
    recommendedName 
      rdf:type Structured_Name
      fullName "Glutamate N-acetyltransferase"
    enzyme enzyme:2.3.1.35
    alternativeName 
      rdf:type Structured_Name
      fullName "Ornithine acetyltransferase"
      shortName "OATase"
    alternativeName 
      rdf:type Structured_Name
      fullName "Ornithine transacetylase"
  domain 
    rdf:type Part
    recommendedName 
      rdf:type Structured_Name
      fullName "Amino-acid acetyltransferase"
    enzyme enzyme:2.3.1.1
    alternativeName 
      rdf:type Structured_Name
      fullName "N-acetylglutamate synthase"
      shortName "AGS"

Changes:

• Protein names are now direct properties of the protein, no intermediate description construct.
• Renamed contains to component.
• Renamed includes to domain.
• Explicit links to enzymes.

GN - Genes

GN   Name=cysA1; Synonyms=cysA; OrderedLocusNames=Rv3117, MT3199;
GN   ORFNames=MTCY164.27;
GN   and
GN   Name=cysA2; OrderedLocusNames=Rv0815c, MT0837; ORFNames=MTV043.07c;

uniprot:O05793
  encodedBy 
    rdf:type Gene
    name "cysA1"
    name "cysA"
    locusName "Rv3117"
    locusName "MT3199"
    orfName "MTCY164.27"
  encodedBy 
    rdf:type Gene
    name "cysA2"
    locusName "Rv0815c"
    locusName "MT0837"
    orfName "MTV043.07c"

OS/OC/OX/OH - Taxonomy

OS   Human immunodeficiency virus type 1 (isolate BRU/LAI group M subtype
OS   B) (HIV-1).
OC   Viruses; Retro-transcribing viruses; Retroviridae; Orthoretrovirinae;
OC   Lentivirus; Primate lentivirus group.
OX   NCBI_TaxID=11686;
OH   NCBI_TaxID=9606; Homo sapiens (Human).

uniprot:P03377
  organism taxon:11686

Changes:

• Taxonomy data is distributed in a separate file (see section on taxonomy), where different types of names can be distinguished reliably.

OG - Gene location

OG   Mitochondrion.
OG   Plasmid pAL2-1.

uniprot:Q01529
  encodedIn Mitochondrion
  encodedIn 
    rdfs:subClassOf Plasmid
    rdfs:label "pAL2-1"

Changes:

• Renamed OG (organelle) to encodedIn to avoid misunderstandings (this is not the subcellular location of the protein, but the location of the gene).

Issues:

• encodedIn should be a property of a Gene, but automatic mapping is not always possible.

R - Citations

RN   [38]
RP   VARIANTS PD GLU-82; CYS-256; TRP-275; GLU-328 AND 441-ARG.
RC   TISSUE=Brain;
RX   MEDLINE=22108846; PubMed=12116199; DOI=10.1002/ajmg.10525;
RG   French Parkinson's disease genetics study group;
RG   European consortium on genetic susceptibility on Parkinson's disease;
RA   West A., Periquet M., Lincoln S., Luecking C.B., Nicholl D.,
RA   Bonifati V., Rawal N., Gasser T., Lohmann E., Deleuze J.-F.,
RA   Maraganore D., Levey A., Wood N.W., Duerr A., Hardy J., Brice A.,
RA   Farrer M.;
RT   "Complex relationship between parkin mutations and Parkinson
RT   disease.";
RL   Am. J. Med. Genet. 114:584-591(2002).
RN   [39]
RP   ERRATUM.
RG   French Parkinson's disease genetics study group;
RG   European consortium on genetic susceptibility on Parkinson's disease;
RA   West A., Periquet M., Lincoln S., Luecking C.B., Nicholl D.,
RA   Bonifati V., Rawal N., Gasser T., Lohmann E., Deleuze J.-F.,
RA   Maraganore D., Levey A., Wood N.W., Duerr A., Hardy J., Brice A.,
RA   Farrer M.J.;
RL   Am. J. Med. Genet. 114:992-992(2002).

uniprot:O60260
  citation <http://purl.uniprot.org/citations/12116199>
    rdf:type Journal_Citation
    title "Complex relationship between parkin mutations and Parkinson disease."
    author "West A."
    author "Periquet M."
    author "Lincoln S."
    author "Luecking C.B."
    author "Nicholl D."
    author "Bonifati V."
    author "Rawal N."
    author "Gasser T."
    author "Lohmann E."
    author "Deleuze J.-F."
    author "Maraganore D."
    author "Levey A."
    author "Wood N.W."
    author "Duerr A."
    author "Hardy J."
    author "Brice A."
    author "Farrer M."
    group "French Parkinson's disease genetics study group"
    group "European consortium on genetic susceptibility on Parkinson's disease"
    owl:sameAs <http://purl.uniprot.org/medline/22108846>
    owl:sameAs <http://purl.uniprot.org/pubmed/12116199>
    <http://purl.org/dc/elements/1.1/identifier> "doi:10.1002/ajmg.10525"
    date 2002
    erratum :1
      rdf:type Journal_Citation
      author "West A."
      author "Periquet M."
      author "Lincoln S."
      author "Luecking C.B."
      author "Nicholl D."
      author "Bonifati V."
      author "Rawal N."
      author "Gasser T."
      author "Lohmann E."
      author "Deleuze J.-F."
      author "Maraganore D."
      author "Levey A."
      author "Wood N.W."
      author "Duerr A."
      author "Hardy J."
      author "Brice A."
      author "Farrer M.J."
      group "French Parkinson's disease genetics study group"
      group "European consortium on genetic susceptibility on Parkinson's disease"
      date 2002
      name "Am. J. Med. Genet."
      volume 114
      pages 992
    name "Am. J. Med. Genet."
    volume 114
    pages "584-591"
    +rdf:type Citation_Statement
    +scope "VARIANTS PD GLU-82; CYS-256; TRP-275; GLU-328 AND 441-ARG"
    +source
      rdf:type Tissue_Source
      name 'Brain'  

Changes:

• Explicit citation subclasses: Journal, Book, Submission, Observation, Patent and Thesis.
• Separated data specific to individual entries from citation data.

Issues:

• Citations are duplicated among entries; a separate citation database would therefore make sense.
• Whenever possible, citations should be linked directly to any relevant data rather than describing the relationship in a scope property.
• Unable to determine which Sources belong together when there are several.
• No ontology for tissues.

How are errata represented?

uniprot:O60260
  citation <http://purl.uniprot.org/citations/12116199>
    rdf:type Journal_Citation
    erratum :1
      rdf:type Journal_Citation

Note that there is no direct connection between the protein and the erratum citation, though the erratum citation may be referenced from parts of the protein. This will simplify maintenance of citations once they are stored in a separate database.

What happened to plasmids in the RC line?

OG   Plasmid F.
..
RC   STRAIN=K12 / CR63; PLASMID=F;

  citation :1
    +context 
      rdf:type Strain
      rdfs:label "K12 / CR63"
  encodedIn 
    rdfs:subClassOf Plasmid
    rdfs:label "F"
    +citation :1

Books:

RA   Kato I., Kohr W.J., Laskowski M. Jr.;
RT   "Evolution of avian ovomucoids.";
RL   (In) Magnusson S., Ottesen M., Foltmann B., Dano K., Neurath H.
RL   (eds.);
RL   Regulatory proteolytic enzymes and their inhibitors, pp.197-206,
RL   Pergamon Press, New York (1978).

uniprot:P68128
  citation 
    rdf:type Book_Citation
    title "Evolution of avian ovomucoids."
    author "Kato I."
    author "Kohr W.J."
    author "Laskowski M. Jr."
    date 1978
    editor "Magnusson S."
    editor "Ottesen M."
    editor "Foltmann B."
    editor "Dano K."
    editor "Neurath H."
    name "Regulatory proteolytic enzymes and their inhibitors"
    pages "197-206"
    publisher "Pergamon Press"
    place "New York"

Database submissions:

RL   Submitted (NOV-1989) to the EMBL/GenBank/DDBJ databases.

uniprot:P0C002
  citation :3
    rdf:type Submission_Citation
    date 1989-11
    submittedTo "EMBL/GenBank/DDBJ"

Unpublished observations:

RL   Unpublished observations (MAR-1996).

uniprot:P52697
  citation 
    rdf:type Observation_Citation
    date 1996-03

Patents:

RL   Patent number EP0290986, 17-NOV-1988.

uniprot:P31668
  citation 
    rdf:type Patent_Citation
    date 1988-11-17
    owl:sameAs <http://purl.uniprot.org/patents/EP0290986>

Theses:

RL   Thesis (1979), University of Stanford, United States.

uniprot:P02283
  citation 
    rdf:type Thesis_Citation
    date 1979
    institution "University of Stanford"
    place "United States"

CC/FT - Annotations

CC   -!- PTM: Characterization of O-linked glycan was studied in Bowes
CC       melanoma cell line.
...
FT   PROPEP       33     35       Removed by plasmin.
FT                                /FTId=PRO_0000028349.

uniprot:P00750
  annotation 
    rdf:type PTM_Annotation
    rdfs:comment 
      "Characterization of O-linked glycan was studied in Bowes melanoma 
       cell line."
  annotation <http://purl.uniprot.org/annotation/PRO_0000028349>
    rdf:type Propeptide_Annotation
    rdfs:comment "Removed by plasmin"
    range 
      rdf:type Range
      begin 33
      end 35

Changes:

• Comments and features are merged into a single hierarchy with various intermediary classes.

Sequence annotation ranges:

1 10?	:r rdf:type Range begin 1 end 10 +rdf:type Endpoint_Statement +certain false
<185 >230	:r rdf:type Range begin 185 +rdf:type Endpoint_Statement +limit false end 230 +rdf:type Endpoint_Statement +limit false
1 ?	:r rdf:type Range begin 1

Sequence change annotations:

There are several types of annotations that indicate differences to other versions of the sequence.

MUTAGEN:

FT   MUTAGEN     137    137       H->N: Binds copper. Forms dimer.
FT   MUTAGEN     717    717       V->C,S: Unchanged beta-APP42/total APP-
FT                                beta ratio.

uniprot:P05067
  annotation 
    rdf:type Mutagenesis_Annotation
    rdfs:comment "Binds copper. Forms dimer"
    range 
      rdf:type Range
      begin 137
      end 137
    substitution "N"
  annotation 
    rdf:type Mutagenesis_Annotation
    rdfs:comment "Unchanged beta-APP42/total APP-beta ratio"
    range 
      rdf:type Range
      begin 717
      end 717
    substitution "C"
    substitution "S"

VAR_SEQ:

FT   VAR_SEQ     781    790       ALMRPGRIDR -> VPPSQTFLLL (in isoform 2).
FT                                /FTId=VSP_033048.
FT   VAR_SEQ     791    893       Missing (in isoform 2).
FT                                /FTId=VSP_033049.

uniprot:Q8NB90
  annotation <http://purl.uniprot.org/annotation/VSP_033048>
    rdf:type Alternative_Sequence_Annotation
    rdfs:comment "In isoform 2."
    range :3
      rdf:type Range
      begin 781
      end 790
    substitution "VPPSQTFLLL"
  annotation <http://purl.uniprot.org/annotation/VSP_033049>
    rdf:type Alternative_Sequence_Annotation
    rdfs:comment "In isoform 2."
    range :4
      rdf:type Range
      begin 791
      end 893
    substitution ""

VARIANT:

FT   VARIANT     296    296       D -> G (in allele TF*D1;
FT                                dbSNP:rs8177238).
FT                                /FTId=VAR_007544.

uniprot:P02787
  annotation <http://purl.uniprot.org/annotation/VAR_007544>
    rdf:type Natural_Variant_Annotation
    rdfs:comment "In allele TF*D1."
    range 
      rdf:type Range
      begin 296
      end 296
    substitution "G"
    rdfs:seeAlso <http://purl.uniprot.org/dbsnp/rs8177238>

CONFLICT:

FT   CONFLICT    541    541       R -> K (in Ref. 1; CAA75675/CAA75676 and
FT                                4; AAH02508).

uniprot:O95671
  annotation 
    rdf:type Sequence_Conflict_Annotation
    range 
      rdf:type Range
      begin 541
      end 541
    substitution "K"
    rdfs:seeAlso <http://purl.uniprot.org/embl/CAA75675>
    rdfs:seeAlso <http://purl.uniprot.org/embl/CAA75676>
    +citation <http://purl.uniprot.org/citations/9736779>
  annotation 
    rdf:type Sequence_Conflict_Annotation
    range 
      rdf:type Range
      begin 541
      end 541
    substitution "K"
    rdfs:seeAlso <http://purl.uniprot.org/embl/AAH02508>
    +citation <http://purl.uniprot.org/citations/15489334>

Changes:

• Feature block is split into separate annotations.

Crosslinks:

FT   CROSSLNK     95    218       Tryptophyl-tyrosyl-methioninium (Trp-Tyr)
FT                                (with M-244).
FT   CROSSLNK    218    244       Tryptophyl-tyrosyl-methioninium (Tyr-Met)
FT                                (with W-95).

uniprot:O59651
  annotation 
    rdf:type Cross-link_Annotation
    rdfs:comment "Tryptophyl-tyrosyl-methioninium (Trp-Tyr) (with M-244)"
    range 
      rdf:type Range
      begin 95
      end 95
    range 
      rdf:type Range
      begin 218
      end 218
  annotation 
    rdf:type Cross-link_Annotation
    rdfs:comment "Tryptophyl-tyrosyl-methioninium (Tyr-Met) (with W-95)"
    range 
      rdf:type Range
      begin 218
      end 218
    range 
      rdf:type Range
      begin 244
      end 244

Mass spectrometry comments:

CC   -!- MASS SPECTROMETRY: Mass=23638.14; Mass_error=3.0;
CC       Method=Electrospray; Range=16-214 (P04653-2); Note=Allele A, with
CC       11 phosphate groups; Source=PubMed:7601973;

uniprot:P04653
  annotation 
    rdf:type Mass_Spectrometry_Annotation
    rdfs:comment "Allele A, with 11 phosphate groups."
    measuredValue 23638.14
    measuredError 3.0
    method ESI
    range 
      rdf:type Range
      begin 16
      end 214
    sequence <http://purl.uniprot.org/isoforms/P04653-2>
    +citation <http://purl.uniprot.org/citations/7601973>

RNA editing comments:

CC   -!- RNA EDITING: Modified_positions=367, 379, 383, 405; Note=Partially
CC       edited.

uniprot:P21521
  annotation 
    rdf:type RNA_Editing_Annotation
    rdfs:comment "Partially edited."
    position 367
    position 379
    position 383
    position 405

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.

uniprot:P14548
  annotation 
    rdf:type RNA_Editing_Annotation
    rdfs:comment 
      "Some positions are modified by RNA editing via nucleotide insertion 
       or deletion. The initiator methionine is created by RNA editing."
    frameshift true

Issues:

• Should link directly to variant annotations, where available.

Sequence caution:

CC   -!- SEQUENCE CAUTION:
CC       Sequence=X07863; Type=Frameshift; Positions=Several;

uniprot:P0A7B3
  annotation 
    rdf:type Frameshift_Annotation
    sequence <http://purl.uniprot.org/embl/X07863>
      rdf:type Genomic_DNA

CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAA39943.1; Type=Miscellaneous discrepancy; Note=Several frameshifts and contaminating sequence;
CC       Sequence=Ref.3; Type=Frameshift; Positions=697;

uniprot:P27612
  annotation 
    rdf:type Sequence_Caution_Annotation
    rdfs:comment "Several frameshifts and contaminating sequence."
    sequence <http://purl.uniprot.org/embl-cds/AAA39943.1>
  annotation 
    rdf:type Frameshift_Annotation
    range 
      rdf:type Range
      begin 697
      end 697
    sequence 
      rdf:type External_Sequence
      citation <http://purl.uniprot.org/citations/7665086>

Changes:

• Comment block is split into separate annotation subclasses.

Biophysicochemical properties:

CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       Absorption:
CC         Abs(max)=~596 nm;
CC         Note=In the presence of anions, the maximum absorption shifts to
CC         about 575 nm;

uniprot:Q48314
  annotation 
    rdf:type Absorption_Annotation
    rdfs:comment "In the presence of anions, the maximum absorption shifts to about 575 nm."
    maximum 596
    certain false

CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       Redox potential:
CC         E(0) is -450 mV for the 3Fe-4S, and -645 mV for the 4Fe-4S
CC         clusters;

uniprot:P00214
  annotation 
    rdf:type Redox_Potential_Annotation
    rdfs:comment "E(0) is -450 mV for the 3Fe-4S, and -645 mV for the 4Fe-4S clusters."

CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       Kinetic parameters:
CC         KM=3.1 mM for N-succinyl-Ala-Ala-Pro-Phe p-nitroanilide (at pH
CC         6.0 with dimethylsulfoxide);
CC         KM=2.3 mM for N-succinyl-Ala-Ala-Pro-Phe p-nitroanilide (at pH
CC         9.0 with dimethylsulfoxide);
CC         KM=1.1 mM for N-succinyl-Ala-Ala-Pro-Phe p-nitroanilide (at pH
CC         9.0 without dimethylsulfoxide);
CC       pH dependence:
CC         Optimum pH is 8.3-9.6;
CC       Temperature dependence:
CC         Optimum temperature is 40 degrees Celsius;

uniprot:P83610
  annotation 
    rdf:type Kinetics_Annotation
    measuredAffinity 
      "3.1 mM for N-succinyl-Ala-Ala-Pro-Phe p-nitroanilide (at pH 6.0 with 
       dimethylsulfoxide)"
    measuredAffinity 
      "2.3 mM for N-succinyl-Ala-Ala-Pro-Phe p-nitroanilide (at pH 9.0 with 
       dimethylsulfoxide)"
    measuredAffinity 
      "1.1 mM for N-succinyl-Ala-Ala-Pro-Phe p-nitroanilide (at pH 9.0 
       without dimethylsulfoxide)"
  annotation 
    rdf:type PH_Dependence_Annotation
    rdfs:comment "Optimum pH is 8.3-9.6."
  annotation 
    rdf:type Temperature_Dependence_Annotation
    rdfs:comment "Optimum temperature is 40 degrees Celsius."

Changes:

• Comment block is split into separate annotation subclasses.

Alternative products:

CC       Event=Alternative splicing; Named isoforms=2;
CC       Name=Long;
CC         IsoId=P51650-1; Sequence=Displayed;
CC       Name=Short;
CC         IsoId=P51650-2; Sequence=VSP_001284;
CC         Note=No experimental confirmation available;
..
FT   VAR_SEQ     107    134       Missing (in isoform Short).
FT                                /FTId=VSP_001284.
SQ   SEQUENCE   523 AA;  56131 MW;  4CA521139C9FA98F CRC64;
     MATCFLLRNF CAARPALRPP GRLLREPAGA QRRSYVGGPA DLHADLLRGD SFVGGRWLPT
     PATFPVYDPA SGAKLGT...

uniprot:P51650
  annotation 
    rdf:type Alternative_Splicing_Annotation
    sequence <http://purl.uniprot.org/isoforms/P51650-1>
    sequence <http://purl.uniprot.org/isoforms/P51650-2>
  annotation <http://purl.uniprot.org/annotation/VSP_001284>
    rdf:type Alternative_Sequence_Annotation
    rdfs:comment "In isoform Short."
    range :2
      rdf:type Range
      begin 107
      end 134
    substitution ""
  annotation 
    rdf:type Caution_Annotation
    rdfs:comment "No experimental confirmation available."
    sequence <http://purl.uniprot.org/isoforms/P51650-2>
  sequence <http://purl.uniprot.org/isoforms/P51650-1>
    rdf:type Simple_Sequence
    modified 2008-04-08
    version 2
    precursor true
    mass 56131
    name "Long"
    rdf:value 
      "MATCFLLRNF CAARPALRPP GRLLREPAGA QRRSYVGGPA DLHADLLRGD SFVGGRWLPT 
       PATFPVYDPA SGAKLGT..."
  sequence <http://purl.uniprot.org/isoforms/P51650-2>
    rdf:type Modified_Sequence
    name "Short"
    basedOn <http://purl.uniprot.org/isoforms/P51650-1>
    modification <http://purl.uniprot.org/annotation/VSP_001284>

Some alternative products comments contain embedded variant, conflict or caution annotations. These are extracted and represented as proper annotation objects that reference the isoforms they are relevant for.

CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing, Alternative initiation; Named isoforms=8;
CC         Comment=Additional isoforms seem to exist;
CC       Name=SV6; Synonyms=p110;
CC         IsoId=Q9UQ88-1; Sequence=Displayed;
CC       Name=SV1; Synonyms=Pbeta21, Beta 2-1;
CC         IsoId=Q9UQ88-2; Sequence=VSP_008286, VSP_008288;
CC         Note=Ref.1 (AAA19594) sequence is in conflict in positions:
CC         109:C->R, 112:H->R;
..

uniprot:Q9UQ88
  annotation 
    rdf:type Alternative_Splicing_Annotation
    rdf:type Alternative_Initiation_Annotation
    rdfs:comment "Additional isoforms seem to exist."
    sequence <http://purl.uniprot.org/isoforms/Q9UQ88-1>
    sequence <http://purl.uniprot.org/isoforms/Q9UQ88-2>
    ...
  annotation 
    rdf:type Sequence_Conflict_Annotation
    range 
      rdf:type Range
      begin 109
      end 109
    substitution "R"
    rdfs:seeAlso <http://purl.uniprot.org/embl/AAA19594>
    sequence <http://purl.uniprot.org/isoforms/Q9UQ88-2>
    +citation <http://purl.uniprot.org/citations/8195233>
  annotation 
    rdf:type Sequence_Conflict_Annotation
    range 
      rdf:type Range
      begin 112
      end 112
    substitution "R"
    rdfs:seeAlso <http://purl.uniprot.org/embl/AAA19594>
    sequence <http://purl.uniprot.org/isoforms/Q9UQ88-2>
    +citation <http://purl.uniprot.org/citations/8195233>
  ...

CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=2;
CC       Name=1; Synonyms=TAF-I alpha;
CC         IsoId=Q01105-1; Sequence=Displayed;
CC       Name=2; Synonyms=TAF-I beta;
CC         IsoId=Q01105-2; Sequence=VSP_009868;
CC         Note=Acetylated on Lys-11. Phosphorylated on Ser-15 and Thr-23.
CC         Variant in position: 4:P->Q (in dbSNP:rs1141138);

uniprot:Q01105
  annotation 
    rdf:type Alternative_Splicing_Annotation
    sequence <http://purl.uniprot.org/isoforms/Q01105-1>
    sequence <http://purl.uniprot.org/isoforms/Q01105-2>
  annotation 
    rdf:type Natural_Variant_Annotation
    range 
      rdf:type Range
      begin 4
      end 4
    substitution "Q"
    rdfs:seeAlso <http://purl.uniprot.org/dbsnp/rs1141138>
    sequence <http://purl.uniprot.org/isoforms/Q01105-2>
  annotation 
    rdf:type Caution_Annotation
    rdfs:comment "Acetylated on Lys-11. Phosphorylated on Ser-15 and Thr-23."
    sequence <http://purl.uniprot.org/isoforms/Q01105-2>

Alternative promoter usage and initiation:

CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative promoter usage, Alternative splicing; Named isoforms=4;
CC       Name=A;
CC         IsoId=Q8WXS8-1; Sequence=Displayed;
CC         Note=Produced by alternative promoter usage;
CC       Name=B;
CC         IsoId=Q8WXS8-2; Sequence=VSP_006958;
CC         Note=Produced by alternative promoter usage;
CC       Name=C;
CC         IsoId=Q8WXS8-3; Sequence=VSP_006958, VSP_005501;
CC         Note=Produced by alternative splicing of isoform B;
CC       Name=D;
CC         IsoId=Q8WXS8-4; Sequence=VSP_005501;
CC         Note=Produced by alternative splicing of isoform A;

uniprot:Q8WXS8
  annotation
    rdf:type Alternative_Promoter_Usage_Annotation
    rdf:type Alternative_Splicing_Annotation
    sequence <http://purl.uniprot.org/isoforms/Q8WXS8-1>
    sequence <http://purl.uniprot.org/isoforms/Q8WXS8-2>
    sequence <http://purl.uniprot.org/isoforms/Q8WXS8-3>
    sequence <http://purl.uniprot.org/isoforms/Q8WXS8-4>
  annotation 
    rdf:type Caution_Annotation
    rdfs:comment "Produced by alternative promoter usage."
    sequence <http://purl.uniprot.org/isoforms/Q8WXS8-1>
  annotation 
    rdf:type Caution_Annotation
    rdfs:comment "Produced by alternative promoter usage."
    sequence <http://purl.uniprot.org/isoforms/Q8WXS8-2>
  annotation 
    rdf:type Caution_Annotation
    rdfs:comment "Produced by alternative splicing of isoform B."
    sequence <http://purl.uniprot.org/isoforms/Q8WXS8-3>
  annotation 
    rdf:type Caution_Annotation
    rdfs:comment "Produced by alternative splicing of isoform A."
    sequence <http://purl.uniprot.org/isoforms/Q8WXS8-4>

Alternative splicing with several unspecified sequences:

CC   -!- ALTERNATIVE PRODUCTS:
CC       Event=Alternative splicing; Named isoforms=5;
CC         Comment=Experimental confirmation may be lacking for some
CC         isoforms;
CC       Name=APP(770);
CC         IsoId=P29216-1; Sequence=Displayed;
CC       Name=APP(395);
CC         IsoId=P29216-2; Sequence=Not described;
CC       Name=APP(563);
CC         IsoId=P29216-3; Sequence=Not described;
..
SQ   SEQUENCE   76 AA;  8527 MW;  492BF3069AB082A1 CRC64;
     EVCSEQAETG PCRAMISRWY FDVTEGKCAP FFYGGCGGNR NNFDTEEYCM AVCGSVMSQS
     LRKTTREPLT RDPVKL
//

uniprot:P29216
  annotation 
    rdf:type Alternative_Splicing_Annotation
    rdfs:comment "Experimental confirmation may be lacking for some isoforms."
    sequence <http://purl.uniprot.org/isoforms/P29216-1>
    sequence <http://purl.uniprot.org/isoforms/P29216-2>
    sequence <http://purl.uniprot.org/isoforms/P29216-3>
    ...
  sequence <http://purl.uniprot.org/isoforms/P29216-1>
    rdf:type Simple_Sequence
    name "APP(770)"
    rdf:value 
      "EVCSEQAETG PCRAMISRWY FDVTEGKCAP FFYGGCGGNR NNFDTEEYCM AVCGSVMSQS 
       LRKTTREPLT RDPVKL"
  sequence <http://purl.uniprot.org/isoforms/P29216-2>
    rdf:type Unknown_Sequence
    name "APP(395)"
  sequence <http://purl.uniprot.org/isoforms/P29216-3>
    rdf:type Unknown_Sequence
    name "APP(563)"
  ...

Pathways:

CC   -!- PATHWAY: Amino-acid biosynthesis; L-lysine biosynthesis via AAA
CC       pathway; L-alpha-aminoadipate from 2-oxoglutarate: step 2/4.

uniprot:P49367
  annotation 
    rdf:type Pathway_Annotation
    rdfs:comment 
      "Amino-acid biosynthesis; L-lysine biosynthesis via AAA pathway; 
       L-alpha-aminoadipate from 2-oxoglutarate: step 2/4."
    +source <http://purl.uniprot.org/unipathway/402.33.12.29>

Notes:

• Added stable identifiers, that connect to separate pathway data set, for (most) pathways.

Web resources:

CC   -!- WEB RESOURCE: Name=Wikipedia; Note=Factor IX entry;
CC       URL="http://en.wikipedia.org/wiki/Factor_IX";
CC   -!- WEB RESOURCE: Name=HAEMB; Note=Hemophilia B mutation database;
CC       URL="http://www.kcl.ac.uk/ip/petergreen/haemBdatabase.html";

uniprot:P00740
  rdfs:seeAlso <http://en.wikipedia.org/wiki/Factor_IX>
    rdf:type Resource
    rdfs:comment "Wikipedia; Factor IX entry"
  rdfs:seeAlso <http://www.kcl.ac.uk/ip/petergreen/haemBdatabase.html>
    rdf:type Resource
    rdfs:comment "HAEMB; Hemophilia B mutation database"

Changes:

• Represented as cross references, not annotations.

Interactions:

CC   -!- INTERACTION:
CC       Self; NbExp=1; IntAct=EBI-77797, EBI-77797;
CC       Q61824:Adam12 (xeno); NbExp=2; IntAct=EBI-77797, EBI-77785;
CC       P03950:ANG; NbExp=3; IntAct=EBI-77797, EBI-525291;
..
DR   IntAct; P35609; 8.

uniprot:P35609
  interaction 
    rdf:type Interaction
    xeno false
    experiments 1
    participant <http://purl.uniprot.org/intact/EBI-77797>
      rdf:type Participant
      owl:sameAs uniprot:P35609
  interaction 
    rdf:type Interaction
    xeno true
    experiments 2
    participant <http://purl.uniprot.org/intact/EBI-77797>
    participant <http://purl.uniprot.org/intact/EBI-77785>
      rdf:type Participant
      rdfs:label "Adam12"
      owl:sameAs uniprot:Q61824
  interaction 
    rdf:type Interaction
    xeno false
    experiments 3
    participant <http://purl.uniprot.org/intact/EBI-77797>
    participant <http://purl.uniprot.org/intact/EBI-525291>
      rdf:type Participant
      rdfs:label "ANG"
      owl:sameAs uniprot:P03950
  rdfs:seeAlso <http://purl.uniprot.org/intact/P35609>
    rdf:type Resource
    database "IntAct"
    rdfs:comment 8

Changes:

• Represented as interactions, not annotations.

DR - Links

Simple example, applies to most types of links:

DR FlyBase; FBgn0010339; 128up.

uniprot:P32234
  rdfs:seeAlso <http://purl.uniprot.org/flybase/FBgn0010339>
    rdf:type Resource
    database "FlyBase"
    rdfs:comment "128up"

For PIR and StyGene, the primary and secondary identifiers are reversed, because only the latter is unique:

DR PIR; S07102; DEBOHS.

uniprot:P14893
  rdfs:seeAlso <http://purl.uniprot.org/pir/DEBOHS>
    rdf:type Resource
    database "PIR"
    rdfs:comment "S07102"

Links to domain databases:

DR   PROSITE; PS00211; ABC_TRANSPORTER_1; FALSE_NEG.
DR   PROSITE; PS50893; ABC_TRANSPORTER_2; 1.
DR   PROSITE; PS51245; MALK; PARTIAL.

DR   PROSITE; PS00010; ASX_HYDROXYL; UNKNOWN_3.

uniprot:P18813
  rdfs:seeAlso <http://purl.uniprot.org/prosite/PS00211>
    rdf:type Resource
    database "PROSITE"
    rdfs:comment "ABC_TRANSPORTER_1"
    +rdf:type Domain_Assignment_Statement
    +falseNegative true
  rdfs:seeAlso <http://purl.uniprot.org/prosite/PS50893>
    rdf:type Resource
    database "PROSITE"
    rdfs:comment "ABC_TRANSPORTER_2"
    +rdf:type Domain_Assignment_Statement
    +hits 1
  rdfs:seeAlso <http://purl.uniprot.org/prosite/PS51245>
    rdf:type Resource
    database "PROSITE"
    rdfs:comment "MALK"
    +rdf:type Domain_Assignment_Statement

uniprot:Q96DN2
  rdfs:seeAlso <http://purl.uniprot.org/prosite/PS00010>
    rdf:type Resource
    database "PROSITE"
    rdfs:comment "ASX_HYDROXYL"
    +rdf:type Domain_Assignment_Statement
    +hits 3
    +certain false

Links to EMBL:

DR   EMBL; AF053231; AAC08355.1; ALT_FRAME; mRNA.
DR   EMBL; BX842680; CAE81952.1; -; Genomic_DNA.
DR   EMBL; AABX02000002; EAA34926.2; ALT_SEQ; Genomic_DNA.

uniprot:O59942
  rdfs:seeAlso <http://purl.uniprot.org/embl-cds/AAC08355.1>
    rdf:type Nucleotide_Resource
    database "EMBL"
    locatedOn <http://purl.uniprot.org/embl/AF053231>
      rdf:type MRNA
    +rdf:type Nucleotide_Mapping_Statement
    +rdfs:comment "Frameshift."
  rdfs:seeAlso <http://purl.uniprot.org/embl-cds/CAE81952.1>
    rdf:type Nucleotide_Resource
    database "EMBL"
    locatedOn <http://purl.uniprot.org/embl/BX842680>
      rdf:type Genomic_DNA
  rdfs:seeAlso <http://purl.uniprot.org/embl-cds/EAA34926.2>
    rdf:type Nucleotide_Resource
    database "EMBL"
    locatedOn <http://purl.uniprot.org/embl/AABX02000002>
      rdf:type Genomic_DNA
    +rdf:type Nucleotide_Mapping_Statement
    +rdfs:comment "Sequence problems."

DR   EMBL; L06463; -; NOT_ANNOTATED_CDS; mRNA.

uniprot:P56593
  rdfs:seeAlso 
    rdf:type Nucleotide_Resource
    database "EMBL"
    locatedOn <http://purl.uniprot.org/embl/L06463>
      rdf:type MRNA

DR   EMBL; BC027387; AAH27387.1; ALT_TERM; mRNA.
DR   EMBL; BC052513; AAH52513.1; ALT_INIT; mRNA.

  rdfs:seeAlso <http://purl.uniprot.org/embl-cds/AAH27387.1>
    rdf:type Nucleotide_Resource
    database "EMBL"
    locatedOn <http://purl.uniprot.org/embl/BC027387>
      rdf:type MRNA
    +rdf:type Nucleotide_Mapping_Statement
    +rdfs:comment "Different termination."
  rdfs:seeAlso <http://purl.uniprot.org/embl-cds/AAH52513.1>
    rdf:type Nucleotide_Resource
    database "EMBL"
    locatedOn <http://purl.uniprot.org/embl/BC052513>
      rdf:type MRNA
    +rdf:type Nucleotide_Mapping_Statement
    +rdfs:comment "Different initiation."

DR   EMBL; X14907; CAA33034.1; -; Genomic_DNA.
DR   EMBL; X14908; CAA33034.1; JOINED; Genomic_DNA.

uniprot:P02668
  rdfs:seeAlso <http://purl.uniprot.org/embl-cds/CAA33034.1>
    rdf:type Nucleotide_Resource
    database "EMBL"
    locatedOn <http://purl.uniprot.org/embl/X14907>
      rdf:type Genomic_DNA
    locatedOn <http://purl.uniprot.org/embl/X14908>
      rdf:type Genomic_DNA

Changes:

• Direct and explicit reference to external resources.
• Database ontology with information from dbxref.txt is integrated into schema.

Issues:

• Describe external resources directly rather than through reification. However: This won't work for domain database hits and status properties.
• rdfs:comment property is not particularly helpful. But: Probably not worth the effort of defining more accurately.
• It is often not clear what the role of the link is; this needs to be made explicit.

Gene Ontology (GO) terms are listed along with the keywords. Also, they have GO specific evidence codes attached to them:

DR   GO; GO:0016514; C:SWI/SNF complex; IDA:UniProtKB.

uniprot:O14497
  classifiedWith go:0016514
    +citation <http://purl.uniprot.org/citations/12200431>
    +status IDA
    +database "UniProtKB"

Notes:

• Added links to citations (data from GOA), where possible.

Multiple references to the same GenomeReviews entry are collapsed:

DR   GenomeReviews; AE005674_GR; S2143.
DR   GenomeReviews; AE014073_GR; S1668.
DR   GenomeReviews; AE014073_GR; S2143.

uniprot:Q7UCD5
  rdfs:seeAlso <http://purl.uniprot.org/genomereviews/AE005674_GR>
    rdf:type Resource
    database "GenomeReviews"
    rdfs:comment "S2143"
  rdfs:seeAlso <http://purl.uniprot.org/genomereviews/AE014073_GR>
    rdf:type Resource
    database "GenomeReviews"
    rdfs:comment "S1668"
    rdfs:comment "S2143"

KW - Keywords

KW   ATP-binding; Chaperone; Membrane; Mitochondrion;
KW   Mitochondrion inner membrane; Nucleotide-binding; Transmembrane.

uniprot:Q5E9H5
  classifiedWith keyword:67
  classifiedWith keyword:143
  classifiedWith keyword:999
  classifiedWith keyword:812

Changes:

• Explicit references using keyword identifiers (see section on keywords).
• If a keyword is higher up in the hierarchy than another keyword that is already mentioned (e.g. Membrane and Mitochondrion inner membrane), it is removed.

SQ - Sequence

DT   01-NOV-1996, sequence version 1.
..
DE   Flags: Precursor;
..
SQ   SEQUENCE   244 AA;  26414 MW;  64D8C6C1204B1018 CRC64;
     MLLLGAVLLL LALPGHDQET TTQGPGVLLP LPKGACTGWM AGIPGHPGHN GAPGRDGRDG
     TPGEKGEKGD PGLIGPKGDI GETGVPGAEG PRGFPGIQGR KGEPGEGAYV YRSAFSVGLE
     TYVTIPNMPI RFTKIFYNQQ NHYDGSTGKF HCNIPGLYYF AYHITVYMKD VKVSLFKKDK
     AMLFTYDQYQ ENNVDQASGS VLLHLEVGDQ VWLQVYGEGE RNGLYADNDN DSTFTGFLLY
     HDTN

uniprot:Q15848
  sequence <http://purl.uniprot.org/isoforms/Q15848-1>
    rdf:type Simple_Sequence
    modified 1996-11-01
    version 1
    precursor true
    mass 26414
    rdf:value 
      "MLLLGAVLLL LALPGHDQET TTQGPGVLLP LPKGACTGWM AGIPGHPGHN GAPGRDGRDG 
       TPGEKGEKGD PGLIGPKGDI GETGVPGAEG PRGFPGIQGR KGEPGEGAYV YRSAFSVGLE 
       TYVTIPNMPI RFTKIFYNQQ NHYDGSTGKF HCNIPGLYYF AYHITVYMKD VKVSLFKKDK 
       AMLFTYDQYQ ENNVDQASGS VLLHLEVGDQ VWLQVYGEGE RNGLYADNDN DSTFTGFLLY 
       HDTN"

Notes:

• Dropped sequence length and checksum. The length can be recomputed faster than it can be read. The checksum can also be computed quite fast, and it is of limited use to outside people as the checksum algorithm we use for historical reasons is not very widespread.
• Every sequence is assigned a globally unique identifier, even if there are no isoforms.

See section on alternative products for more examples.

EV - Evidence Tags

Evidence tags are attached directly to statements:

uniprot:P15529
  annotation 
    rdf:type PTM_Annotation
    rdfs:comment 
      "Extensively O-glycosylated in the Ser/Thr-rich domain. 
       O-glycosylation is required for Neisseria binding but not for 
       Measles virus or human adenovirus binding."
    +source <http://purl.uniprot.org/citations/12112588>
    +source <http://purl.uniprot.org/citations/15307194>

UniRef

Following is a sample entry in XML syntax (see DTD of the original XML format).

<entry id="UniRef50_Q8WZ42" updated="2008-12-16">
<name>Cluster: Titin</name>
<property type="member count" value="82" />
<property type="common taxon" value="Eukaryota" />
<property type="common taxon ID" value="2759" />
<representativeMember>
<dbReference type="UniProtKB ID" id="TITIN_HUMAN"><property type="UniProtKB accession" value="Q8WZ42" />
<property type="UniParc ID" value="UPI0000D7E631" />
<property type="UniRef100 ID" value="UniRef100_Q8WZ42" />
<property type="UniRef90 ID" value="UniRef90_Q8WZ42" />
<property type="protein name" value="Titin" />
<property type="source organism" value="Homo sapiens (Human)" />
<property type="NCBI taxonomy" value="9606" />
<property type="length" value="34350" />
</dbReference>
<sequence length="34350" checksum="2558BCFE2922B347">
MTTQAPTFTQPLQSVVVLEGSTATFEA..."
</sequence>
</representativeMember>
<member>
<dbReference type="UniProtKB ID" id="Q8WZ42-8"><property type="UniProtKB accession" value="Q8WZ42-8" />
<property type="UniParc ID" value="UPI0000D7E637" />
<property type="UniRef100 ID" value="UniRef100_Q8WZ42-8" />
<property type="UniRef90 ID" value="UniRef90_Q8WZ42" />
<property type="protein name" value="Isoform 8 of Titin" />
<property type="source organism" value="Homo sapiens (Human)" />
<property type="NCBI taxonomy" value="9606" />
<property type="length" value="34474" />
</dbReference>
</member>
...

uniref:UniRef50_Q8WZ42
  rdf:type Cluster
  rdfs:label "Cluster: Titin"
  similarity 0.5
  identity 0.5
  modified 2008-12-16
  commonTaxon <http://purl.uniprot.org/taxonomy/2759>
  member 
    rdf:type Sequence
    owl:sameAs <http://purl.uniprot.org/uniparc/UPI0000D7E631>
    sequenceFor <http://purl.uniprot.org/uniprot/Q8WZ42>
    mnemonic "TITIN_HUMAN"
    reviewed true
    rdfs:label "Titin"
    memberOf uniref:UniRef100_Q8WZ42
    memberOf uniref:UniRef90_Q8WZ42
    organism <http://purl.uniprot.org/taxonomy/9606>
    length 34350
    representativeFor uniref:UniRef50_Q8WZ42
    sequence 
      "MTTQAPTFTQ PLQSVVVLEG STATFEA..."
  member 
    rdf:type Sequence
    owl:sameAs <http://purl.uniprot.org/uniparc/UPI0000D7E637>
    owl:sameAs <http://purl.uniprot.org/isoforms/Q8WZ42-8>
    reviewed true
    rdfs:label "Isoform 8 of Titin"
    memberOf uniref:UniRef100_Q8WZ42-8
    memberOf uniref:UniRef90_Q8WZ42
    organism <http://purl.uniprot.org/taxonomy/9606>
    length 34474
...

Changes:

• Reduced the amount of data that is duplicated from the UniProt data set.
• All data is distributed in a single file rather than one file per similarity level.

UniParc

Here is a sample entry in the original XML format (currently not distributed):

<entry accession="UPI0000000001">
<dbReferenceList>
    <dbReference db="EMBL" id="AAF63732" version="1" version_i="1" active="Y" created="12-Mar-2003" last="02-Se
p-2008" NCBI_GI="7546898" NCBI_taxonomy_id="10245"/>
    <dbReference db="EMBL" id="CAD90637" version="1" version_i="1" active="Y" created="16-Jun-2003" last="02-Se
p-2008" NCBI_GI="30519462" NCBI_taxonomy_id="10243"/>
...
</dbReferenceList>
<sequence length="250" crc64="28FE89850863372D">
MGAAASIQTTVNTLSERISSKLEQEANASAQTKCDIEIGNFYIRQNHGCNLTVKNMCSAD
ADAQLDAVLSAATETYSGLTPEQKAYVPAMFTAALNIQTSVNTVVRDFENYVKQTCNSSA
VVDNKLKIQNVIIDECYGAPGSPTNLEFINTGSSKGNCAIKALMQLTTKATTQIAPKQVA
GTGVQFYMIVIGVIILAALFMYYAKRMLFTSTNDKIKLILANKENVHWTTYMDTFFRTSP
MVIATTDMQN
</sequence>
</entry>

Here is the RDF version of the same data:

uniparc:UPI0000000001
  rdf:type Sequence
  sequenceFor <http://purl.uniprot.org/embl-cds/AAF63732.1>
    organism <http://purl.uniprot.org/taxonomy/10245>
    rdfs:seeAlso <http://purl.uniprot.org/gi/7546898>
    +version 1
    +created 2003-03-12
    +modified 2008-09-02
  sequenceFor <http://purl.uniprot.org/embl-cds/CAD90637.1>
    organism <http://purl.uniprot.org/taxonomy/10243>
    rdfs:seeAlso <http://purl.uniprot.org/gi/30519462>
    +version 1
    +created 2003-06-16
    +modified 2008-09-02
...
  rdf:value 
    "MGAAASIQTT VNTLSERISS KLEQEANASA QTKCDIEIGN FYIRQNHGCN LTVKNMCSAD 
     ADAQLDAVLS AATETYSGLT PEQKAYVPAM FTAALNIQTS VNTVVRDFEN YVKQTCNSSA 
     VVDNKLKIQN VIIDECYGAP GSPTNLEFIN TGSSKGNCAI KALMQLTTKA TTQIAPKQVA 
     GTGVQFYMIV IGVIILAALF MYYAKRMLFT STNDKIKLIL ANKENVHWTT YMDTFFRTSP 
     MVIATTDMQN"

Notes:

• Some of the identifiers include version numbers.
• No new classes and properties had to be created for describing this data set.
• Dropped internal version number and sequence attributes. The sequence length can be recomputed faster than it can be read. The checksum can also be computed quite fast, and it is of limited use to outside people as the checksum algorithm we use for historical reasons is not very widespread.

Keywords

ID   Membrane.
AC   KW-0472
DE   Protein which is membrane-bound or membrane-associated. A membrane is
DE   the layer which forms the boundary of cells and intracellular
DE   organelles. It is composed of two oriented lipid layers in which
DE   proteins are embedded and acts as a selective permeability barrier.
GO   GO:0016020; membrane
HI   Cellular component: Membrane.
CA   Cellular component.
//
ID   Mitochondrion inner membrane.
AC   KW-0999
DE   Protein found in or associated with the inner membrane of a
DE   mitochondrion, the membrane which separates the mitochondrial matrix
DE   from the intermembrane space.
SY   Mitochondrial inner membrane; Inner mitochondrial membrane.
HI   Cellular component: Membrane; Mitochondrion inner membrane.
HI   Cellular component: Mitochondrion; Mitochondrion inner membrane.
CA   Cellular component.
//
IC   Cellular component.
AC   KW-9998
DE   Keywords assigned to proteins because they are found in a specific
DE   cellular or extracellular component.
//

keyword:472
  rdf:type Concept
  rdfs:label "Membrane"
  rdfs:comment 
    "Protein which is membrane-bound or membrane-associated. A membrane is 
     the layer which forms the boundary of cells and intracellular 
     organelles. It is composed of two oriented lipid layers in which 
     proteins are embedded and acts as a selective permeability barrier."
  rdfs:subClassOf keyword:9998
  owl:sameAs <http://purl.uniprot.org/go/0016020>
keyword:999
  rdf:type Concept
  rdfs:label "Mitochondrion inner membrane"
  rdfs:label "Mitochondrial inner membrane"
  rdfs:label "Inner mitochondrial membrane"
  rdfs:comment 
    "Protein found in or associated with the inner membrane of a 
     mitochondrion, the membrane which separates the mitochondrial matrix 
     from the intermembrane space."
  rdfs:subClassOf keyword:472
  rdfs:subClassOf keyword:496
keyword:9998
  rdf:type Concept
  rdfs:label "Cellular component"
  rdfs:comment 
    "Keywords assigned to proteins because they are found in a specific 
     cellular or extracellular component."

Notes:

• Categories (CA) are handled as (top level) keywords.

Note that keywords are both classes and instances. This allows us to make the hierarchy explicitly through use of owl:subClassOf, without loosing the ability to create restrictions such as someProperty rdfs:range Keyword. Having classes that are instances as well is allowed in OWL Full.

Enzymes

[enzclass.txt]
1. -. -.-  Oxidoreductases.
1. 1. -.-   Acting on the CH-OH group of donors.
1. 1. 1.-    With NAD(+) or NADP(+) as acceptor.

[enzyme.dat]
ID   1.1.1.1
DE   Alcohol dehydrogenase.
AN   Aldehyde reductase.
CA   An alcohol + NAD(+) = an aldehyde or ketone + NADH.
CF   Iron or zinc.
CC   -!- Acts on primary or secondary alcohols or hemiacetals.
CC   -!- The animal, but not the yeast, enzyme acts also on cyclic secondary
CC       alcohols.
PR   PROSITE; PDOC00058;
PR   PROSITE; PDOC00059;
PR   PROSITE; PDOC00060;
DR   P07327, ADH1A_HUMAN;  P28469, ADH1A_MACMU;  Q5RBP7, ADH1A_PONAB;
..

enzyme:1.-.-.-
  rdf:type Enzyme
  name "Oxidoreductases"

enzyme:1.1.-.-
  rdf:type Enzyme
  name "Acting on the CH-OH group of donors"
  rdfs:subClassOf enzyme:1.-.-.-

enzyme:1.1.1.-
  rdf:type Enzyme
  name "With NAD(+) or NADP(+) as acceptor"
  rdfs:subClassOf enzyme:1.1.-.-

enzyme:1.1.1.1
  rdf:type Enzyme
  name "Alcohol dehydrogenase"
  name "Aldehyde reductase"
  activity "An alcohol + NAD(+) = an aldehyde or ketone + NADH."
  cofactor "Zinc or Iron."
  rdfs:comment "Acts on primary or secondary alcohols or hemiacetals."
  rdfs:comment "The animal, but not the yeast, enzyme acts also on cyclic secondary alcohols."
  rdfs:subClassOf enzyme:1.1.1.-

Changes:

• Single file for all levels of enzyme classes.
• Dropped cross references, they should already be available in the other direction.
• Hierarchy is made explicit, even though it may be obvious to human readers.

Gene Ontology

DTD for the original format

go:GO:0016209
  rdf:type term
  accession GO:0016209
  name "antioxidant activity"
  definition "Inhibition of the reactions brought about by ..."
  synonym "some synonym"
  is_a go:GO:0003674
  dbxref
    database_symbol "InterPro"
    reference "IPR000866"
...
go:GO:0009492
  rdf:type term
  accession GO:0009492
  name "2Fe-2S electron transfer carrier"
  definition "OBSOLETE (was not defined before being made obsolete)."
  is_a go:obsolete_molecular_function

go:0016209
  rdf:type Concept
  rdfs:label "antioxidant activity"
  rdfs:comment "Inhibition of the reactions brought about by ..."
  rdfs:subClassOf go:0003674
...
go:0009492
  rdf:type Concept
  obsolete true
  rdfs:label "2Fe-2S electron transfer carrier"

Even though GO is already distributed in RDF format, some changes were made:

• Explicit hierarchy.
• Removed GO: prefix from identifiers, as colons have a special meaning within URNs.
• Dropped outgoing references.

Taxonomy

taxon:11686
  rdf:type Taxon
  reviewed true
  mnemonic "HV1BR"
  scientificName "Human immunodeficiency virus type 1 (isolate BRU/LAI group M subtype B)"
  commonName "HIV-1"
  otherName "Human immunodeficiency virus type 1 (BRU ISOLATE)"
  host taxon:9606
  rdfs:subClassOf taxon:540993
  partOfLineage false

Note that taxa with partOfLineage false are omitted from the lineage displayed in flat text UniProt entries.

Pathways

pathway:402.33.12.29
  rdf:type Pathway
  rdfs:label 
    "Amino-acid biosynthesis; L-lysine biosynthesis via AAA pathway;
     L-alpha-aminoadipate from 2-oxoglutarate: step 2/4"
  rdfs:subClassOf pathway:402.33.12

This data is extracted and referenced from the main UniProt data set.

© 2009 Swiss Institute of Bioinformatics. All rights reserved. Last modified December 16, 2008.