Documentation for Human Mitochondrial Protein Database Data Elements

Schema MITO.xsd

Element MITODB_ID
diagram
children SWISSPROT_ID DESCRIPTION PROTEIN_NAME GENE ALIASES LOCATION KEY_WORDS TISSUE DISEASE FUNCTION SIMILARITY CHROM_LOCATION DATABASE_LINKS PROTEIN_SEQUENCE REFERENCE
annotation
documentation 
Human Mitochondrial Database MITODB ID. Created by Ravi on 02-17-03
source 
<xs:element name="MITODB_ID">
  <xs:annotation>
    <xs:documentation>Human Mitochondrial Database MITODB ID. Created by Ravi on 02-17-03</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:sequence>
      <xs:element name="SWISSPROT_ID">
        <xs:annotation>
          <xs:documentation>This swiss prot id/TREMBL id is unique for each entry. </xs:documentation>
        </xs:annotation>
      </xs:element>
      <xs:element name="DESCRIPTION" type="xs:string" minOccurs="0">
        <xs:annotation>
          <xs:documentation>Description of the Protein Name</xs:documentation>
        </xs:annotation>
      </xs:element>
      <xs:element name="PROTEIN_NAME" type="xs:string">
        <xs:annotation>
          <xs:documentation>Most commonly used name for a protein.</xs:documentation>
        </xs:annotation>
      </xs:element>
      <xs:element name="GENE" type="xs:string" minOccurs="0">
        <xs:annotation>
          <xs:documentation>Gene name of a protein</xs:documentation>
        </xs:annotation>
      </xs:element>
      <xs:element name="ALIASES" type="xs:string" minOccurs="0">
        <xs:annotation>
          <xs:documentation>Aliases for protein. Only used from the SwissProt and LocusLink. Ravi's aliases need to be updated.</xs:documentation>
        </xs:annotation>
      </xs:element>
      <xs:element name="LOCATION" type="xs:string" minOccurs="0">
        <xs:annotation>
          <xs:documentation>Location of mitochondrion where  mitochondrial protein is localized. </xs:documentation>
        </xs:annotation>
      </xs:element>
      <xs:element name="KEY_WORDS" type="xs:string" minOccurs="0">
        <xs:annotation>
          <xs:documentation>Key words with any one of the data items belong to mitochondrion (eg: Exercise intolerence)</xs:documentation>
        </xs:annotation>
      </xs:element>
      <xs:element name="TISSUE" type="xs:string" minOccurs="0">
        <xs:annotation>
          <xs:documentation>Tissue in which mitochondrial protein is expressed.</xs:documentation>
        </xs:annotation>
      </xs:element>
      <xs:element name="DISEASE" type="xs:string" minOccurs="0">
        <xs:annotation>
          <xs:documentation>If a mitochondrial protein is shown to be involved withany disease, its role is explained.</xs:documentation>
        </xs:annotation>
      </xs:element>
      <xs:element name="FUNCTION" type="xs:string" minOccurs="0">
        <xs:annotation>
          <xs:documentation>Cellular function of a mitochondrial protein.</xs:documentation>
        </xs:annotation>
      </xs:element>
      <xs:element name="SIMILARITY" type="xs:string" minOccurs="0">
        <xs:annotation>
          <xs:documentation>Similarity with other protein is explained.</xs:documentation>
        </xs:annotation>
      </xs:element>
      <xs:element name="CHROM_LOCATION" type="xs:string" minOccurs="0">
        <xs:annotation>
          <xs:documentation>Chromosomal location of nuclear encoded mitochondrial proteins.</xs:documentation>
        </xs:annotation>
      </xs:element>
      <xs:element name="DATABASE_LINKS" minOccurs="0">
        <xs:annotation>
          <xs:documentation>Available external Database links to a mitochondrial protein.</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:sequence>
            <xs:element name="EC_NUMBER" type="xs:string" minOccurs="0">
              <xs:annotation>
                <xs:documentation>Enzyme Commision (EC) number for enzyme</xs:documentation>
              </xs:annotation>
            </xs:element>
            <xs:element name="OMIM_LINK" type="xs:string" minOccurs="0">
              <xs:annotation>
                <xs:documentation>Link to OMIM site: http://www.ncbi.nlm.nih.gov/omim/</xs:documentation>
              </xs:annotation>
            </xs:element>
            <xs:element name="REF_SEQ" type="xs:string" minOccurs="0">
              <xs:annotation>
                <xs:documentation>Link to RefSeq site: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=Nucleotide</xs:documentation>
              </xs:annotation>
            </xs:element>
            <xs:element name="LOCUS_LINK" type="xs:string" minOccurs="0">
              <xs:annotation>
                <xs:documentation>Link to LocusLink site: http://www.ncbi.nlm.nih.gov/LocusLink/</xs:documentation>
              </xs:annotation>
            </xs:element>
            <xs:element name="GDB_ID" type="xs:string" minOccurs="0">
              <xs:annotation>
                <xs:documentation>Link to GDB site: http://gdbwww.gdb.org</xs:documentation>
              </xs:annotation>
            </xs:element>
            <xs:element name="PUBMED_ID" type="xs:string" minOccurs="0">
              <xs:annotation>
                <xs:documentation>Link to PubMed site: http://www.ncbi.nlm.nih.gov/entrez</xs:documentation>
              </xs:annotation>
            </xs:element>
            <xs:element name="TWO_D_LINK" type="xs:string" minOccurs="0">
              <xs:annotation>
                <xs:documentation>2-D info at SwissProt site: http://us.expasy.org/cgi-bin/nice2dpage.pl</xs:documentation>
              </xs:annotation>
            </xs:element>
          </xs:sequence>
        </xs:complexType>
      </xs:element>
      <xs:element name="PROTEIN_SEQUENCE" minOccurs="0">
        <xs:annotation>
          <xs:documentation>Amino acid sequence of protein.</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:sequence>
            <xs:element name="AA_LENGTH" type="xs:int" minOccurs="0">
              <xs:annotation>
                <xs:documentation>Length is calculated from the sequence.</xs:documentation>
              </xs:annotation>
            </xs:element>
            <xs:element name="pI" type="xs:float" minOccurs="0">
              <xs:annotation>
                <xs:documentation>Tentative pI is calculated from the amino acid sequence.</xs:documentation>
              </xs:annotation>
            </xs:element>
            <xs:element name="MOL_WT" type="xs:float" minOccurs="0">
              <xs:annotation>
                <xs:documentation>Molecular weight is calculated from the sequence.</xs:documentation>
              </xs:annotation>
            </xs:element>
            <xs:element name="SEQ" type="xs:string" minOccurs="0">
              <xs:annotation>
                <xs:documentation>Protein sequence is derived from the SwissProt.</xs:documentation>
              </xs:annotation>
            </xs:element>
            <xs:element name="VARIANTS" minOccurs="0" maxOccurs="unbounded">
              <xs:annotation>
                <xs:documentation>Variants of a protein sequence is explained with reference.</xs:documentation>
              </xs:annotation>
              <xs:complexType>
                <xs:sequence>
                  <xs:element name="VARIANT" type="xs:string" minOccurs="0"/>
                  <xs:element name="AA_START" type="xs:int" minOccurs="0"/>
                  <xs:element name="AA_END" type="xs:int" minOccurs="0"/>
                  <xs:element name="DETAILS" type="xs:string" minOccurs="0"/>
                </xs:sequence>
              </xs:complexType>
            </xs:element>
          </xs:sequence>
        </xs:complexType>
      </xs:element>
      <xs:element name="REFERENCE" minOccurs="0" maxOccurs="unbounded">
        <xs:annotation>
          <xs:documentation>Reference(s) associated with each of mitochondrial protein.</xs:documentation>
        </xs:annotation>
        <xs:complexType>
          <xs:sequence>
            <xs:element name="AUTHORS" type="xs:string" minOccurs="0">
              <xs:annotation>
                <xs:documentation>Author Names fo the reference. Needs to be separated into individual authors.</xs:documentation>
              </xs:annotation>
            </xs:element>
            <xs:element name="TITLE" type="xs:string" minOccurs="0">
              <xs:annotation>
                <xs:documentation>Title of the reference.</xs:documentation>
              </xs:annotation>
            </xs:element>
            <xs:element name="JOURNAL" type="xs:string" minOccurs="0">
              <xs:annotation>
                <xs:documentation>Journal Name with Volume, Year, Page numbers of the reference. Needs to be separated into individual tokens.</xs:documentation>
              </xs:annotation>
            </xs:element>
          </xs:sequence>
        </xs:complexType>
      </xs:element>
    </xs:sequence>
  </xs:complexType>
</xs:element>

element MITODB_ID/SWISSPROT_ID
diagram
annotation
documentation 
This swiss prot id/TREMBL id is unique for each entry.
source 
<xs:element name="SWISSPROT_ID">
  <xs:annotation>
    <xs:documentation>This swiss prot id/TREMBL id is unique for each entry. </xs:documentation>
  </xs:annotation>
</xs:element>

element MITODB_ID/DESCRIPTION
diagram
type xs:string
annotation
documentation 
Description of the Protein Name
source 
<xs:element name="DESCRIPTION" type="xs:string" minOccurs="0">
  <xs:annotation>
    <xs:documentation>Description of the Protein Name</xs:documentation>
  </xs:annotation>
</xs:element>

element MITODB_ID/PROTEIN_NAME
diagram
type xs:string
annotation
documentation 
Most commonly used name for a protein.
source 
<xs:element name="PROTEIN_NAME" type="xs:string">
  <xs:annotation>
    <xs:documentation>Most commonly used name for a protein.</xs:documentation>
  </xs:annotation>
</xs:element>

element MITODB_ID/GENE
diagram
type xs:string
annotation
documentation 
Gene name of a protein
source 
<xs:element name="GENE" type="xs:string" minOccurs="0">
  <xs:annotation>
    <xs:documentation>Gene name of a protein</xs:documentation>
  </xs:annotation>
</xs:element>

element MITODB_ID/ALIASES
diagram
type xs:string
annotation
documentation 
Aliases for protein. Only used from the SwissProt and LocusLink. Ravi's aliases need to be updated.
source 
<xs:element name="ALIASES" type="xs:string" minOccurs="0">
  <xs:annotation>
    <xs:documentation>Aliases for protein. Only used from the SwissProt and LocusLink. Ravi's aliases need to be updated.</xs:documentation>
  </xs:annotation>
</xs:element>

element MITODB_ID/LOCATION
diagram
type xs:string
annotation
documentation 
Location of mitochondrion where  mitochondrial protein is localized.
source 
<xs:element name="LOCATION" type="xs:string" minOccurs="0">
  <xs:annotation>
    <xs:documentation>Location of mitochondrion where  mitochondrial protein is localized. </xs:documentation>
  </xs:annotation>
</xs:element>

element MITODB_ID/KEY_WORDS
diagram
type xs:string
annotation
documentation 
Key words with any one of the data items belong to mitochondrion (eg: Exercise intolerence)
source 
<xs:element name="KEY_WORDS" type="xs:string" minOccurs="0">
  <xs:annotation>
    <xs:documentation>Key words with any one of the data items belong to mitochondrion (eg: Exercise intolerence)</xs:documentation>
  </xs:annotation>
</xs:element>

element MITODB_ID/TISSUE
diagram
type xs:string
annotation
documentation 
Tissue in which mitochondrial protein is expressed.
source 
<xs:element name="TISSUE" type="xs:string" minOccurs="0">
  <xs:annotation>
    <xs:documentation>Tissue in which mitochondrial protein is expressed.</xs:documentation>
  </xs:annotation>
</xs:element>

element MITODB_ID/DISEASE
diagram
type xs:string
annotation
documentation 
If a mitochondrial protein is shown to be involved withany disease, its role is explained.
source 
<xs:element name="DISEASE" type="xs:string" minOccurs="0">
  <xs:annotation>
    <xs:documentation>If a mitochondrial protein is shown to be involved withany disease, its role is explained.</xs:documentation>
  </xs:annotation>
</xs:element>

element MITODB_ID/FUNCTION
diagram
type xs:string
annotation
documentation 
Cellular function of a mitochondrial protein.
source 
<xs:element name="FUNCTION" type="xs:string" minOccurs="0">
  <xs:annotation>
    <xs:documentation>Cellular function of a mitochondrial protein.</xs:documentation>
  </xs:annotation>
</xs:element>

element MITODB_ID/SIMILARITY
diagram
type xs:string
annotation
documentation 
Similarity with other protein is explained.
source 
<xs:element name="SIMILARITY" type="xs:string" minOccurs="0">
  <xs:annotation>
    <xs:documentation>Similarity with other protein is explained.</xs:documentation>
  </xs:annotation>
</xs:element>

element MITODB_ID/CHROM_LOCATION
diagram
type xs:string
annotation
documentation 
Chromosomal location of nuclear encoded mitochondrial proteins.
source 
<xs:element name="CHROM_LOCATION" type="xs:string" minOccurs="0">
  <xs:annotation>
    <xs:documentation>Chromosomal location of nuclear encoded mitochondrial proteins.</xs:documentation>
  </xs:annotation>
</xs:element>

element MITODB_ID/DATABASE_LINKS
diagram
children EC_NUMBER OMIM_LINK REF_SEQ LOCUS_LINK GDB_ID PUBMED_ID TWO_D_LINK
annotation
documentation 
Available external Database links to a mitochondrial protein.
source 
<xs:element name="DATABASE_LINKS" minOccurs="0">
  <xs:annotation>
    <xs:documentation>Available external Database links to a mitochondrial protein.</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:sequence>
      <xs:element name="EC_NUMBER" type="xs:string" minOccurs="0">
        <xs:annotation>
          <xs:documentation>Enzyme Commision (EC) number for enzyme</xs:documentation>
        </xs:annotation>
      </xs:element>
      <xs:element name="OMIM_LINK" type="xs:string" minOccurs="0">
        <xs:annotation>
          <xs:documentation>Link to OMIM site: http://www.ncbi.nlm.nih.gov/omim/</xs:documentation>
        </xs:annotation>
      </xs:element>
      <xs:element name="REF_SEQ" type="xs:string" minOccurs="0">
        <xs:annotation>
          <xs:documentation>Link to RefSeq site: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=Nucleotide</xs:documentation>
        </xs:annotation>
      </xs:element>
      <xs:element name="LOCUS_LINK" type="xs:string" minOccurs="0">
        <xs:annotation>
          <xs:documentation>Link to LocusLink site: http://www.ncbi.nlm.nih.gov/LocusLink/</xs:documentation>
        </xs:annotation>
      </xs:element>
      <xs:element name="GDB_ID" type="xs:string" minOccurs="0">
        <xs:annotation>
          <xs:documentation>Link to GDB site: http://gdbwww.gdb.org</xs:documentation>
        </xs:annotation>
      </xs:element>
      <xs:element name="PUBMED_ID" type="xs:string" minOccurs="0">
        <xs:annotation>
          <xs:documentation>Link to PubMed site: http://www.ncbi.nlm.nih.gov/entrez</xs:documentation>
        </xs:annotation>
      </xs:element>
      <xs:element name="TWO_D_LINK" type="xs:string" minOccurs="0">
        <xs:annotation>
          <xs:documentation>2-D info at SwissProt site: http://us.expasy.org/cgi-bin/nice2dpage.pl</xs:documentation>
        </xs:annotation>
      </xs:element>
    </xs:sequence>
  </xs:complexType>
</xs:element>

element MITODB_ID/DATABASE_LINKS/EC_NUMBER
diagram
type xs:string
annotation
documentation 
Enzyme Commision (EC) number for enzyme
source 
<xs:element name="EC_NUMBER" type="xs:string" minOccurs="0">
  <xs:annotation>
    <xs:documentation>Enzyme Commision (EC) number for enzyme</xs:documentation>
  </xs:annotation>
</xs:element>

element MITODB_ID/DATABASE_LINKS/OMIM_LINK
diagram
type xs:string
annotation
documentation 
Link to OMIM site: http://www.ncbi.nlm.nih.gov/omim/
source 
<xs:element name="OMIM_LINK" type="xs:string" minOccurs="0">
  <xs:annotation>
    <xs:documentation>Link to OMIM site: http://www.ncbi.nlm.nih.gov/omim/</xs:documentation>
  </xs:annotation>
</xs:element>

element MITODB_ID/DATABASE_LINKS/REF_SEQ
diagram
type xs:string
annotation
documentation 
Link to RefSeq site: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=Nucleotide
source 
<xs:element name="REF_SEQ" type="xs:string" minOccurs="0">
  <xs:annotation>
    <xs:documentation>Link to RefSeq site: http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=Nucleotide</xs:documentation>
  </xs:annotation>
</xs:element>

element MITODB_ID/DATABASE_LINKS/LOCUS_LINK
diagram
type xs:string
annotation
documentation 
Link to LocusLink site: http://www.ncbi.nlm.nih.gov/LocusLink/
source 
<xs:element name="LOCUS_LINK" type="xs:string" minOccurs="0">
  <xs:annotation>
    <xs:documentation>Link to LocusLink site: http://www.ncbi.nlm.nih.gov/LocusLink/</xs:documentation>
  </xs:annotation>
</xs:element>

element MITODB_ID/DATABASE_LINKS/GDB_ID
diagram
type xs:string
annotation
documentation 
Link to GDB site: http://gdbwww.gdb.org
source 
<xs:element name="GDB_ID" type="xs:string" minOccurs="0">
  <xs:annotation>
    <xs:documentation>Link to GDB site: http://gdbwww.gdb.org</xs:documentation>
  </xs:annotation>
</xs:element>

element MITODB_ID/DATABASE_LINKS/PUBMED_ID
diagram
type xs:string
annotation
documentation 
Link to PubMed site: http://www.ncbi.nlm.nih.gov/entrez
source 
<xs:element name="PUBMED_ID" type="xs:string" minOccurs="0">
  <xs:annotation>
    <xs:documentation>Link to PubMed site: http://www.ncbi.nlm.nih.gov/entrez</xs:documentation>
  </xs:annotation>
</xs:element>

element MITODB_ID/DATABASE_LINKS/TWO_D_LINK
diagram
type xs:string
annotation
documentation 
2-D info at SwissProt site: http://us.expasy.org/cgi-bin/nice2dpage.pl
source 
<xs:element name="TWO_D_LINK" type="xs:string" minOccurs="0">
  <xs:annotation>
    <xs:documentation>2-D info at SwissProt site: http://us.expasy.org/cgi-bin/nice2dpage.pl</xs:documentation>
  </xs:annotation>
</xs:element>

element MITODB_ID/PROTEIN_SEQUENCE
diagram
children AA_LENGTH pI MOL_WT SEQ VARIANTS
annotation
documentation 
Amino acid sequence of protein.
source 
<xs:element name="PROTEIN_SEQUENCE" minOccurs="0">
  <xs:annotation>
    <xs:documentation>Amino acid sequence of protein.</xs:documentation>
  </xs:annotation>
  <xs:complexType>
    <xs:sequence>
      <xs:element name="AA_LENGTH" type="xs:int" minOccurs="0">
        <xs:annotation>
          <xs:documentation>Length is calculated from the sequence.</xs:documentation>