text: user1586: In creating a parser for the UniProt flat file uniprot_sprot.dat (directory) in the manual for the section SUBCELLULAR LOCATION is listed 
  
  The format of SUBCELLULAR LOCATION is:
  CC   -!- SUBCELLULAR LOCATION:(( Molecule:)?( Location.)+)?(
    Note=Free_text( Flag)?.)?
  Where:  
  
  Molecule: Isoform, chain or peptide name  
  Location = Subcellular_location( Flag)?(; Topology( Flag)?)?(; Orientation( Flag)?)? 
    
    
  Subcellular_location: SL-line of subcell.txt ID-record 
  Topology: SL-line of subcell.txt IT-record 
  Orientation: SL-line of subcell.txt IO-record
  
  
  
  What does Flag mean?
  My best guess at present is that these are the text surrounded by parenthesis, e.g.
   Note=Not associated with microtubules (PubMed:21558460).
  
  but that does not help in understanding why it is named flag.
  While I can use my parser to verify this is correct when this section is working, it would be nicer to have a better understanding of what the word flag means in this context.
  I also checked the XML schema but no help there.
  
  Per request.
  More examples from file.
  These where gathered using grep. 
  grep -A 3 -n 'CC   -!- SUBCELLULAR LOCATION'  /mnt/.../uniprot_sprot.dat     
  
  
  71:CC   -!- SUBCELLULAR LOCATION: Host membrane {ECO:0000305}; Single-pass
  72-CC       membrane protein {ECO:0000305}.
  
  2163:CC   -!- SUBCELLULAR LOCATION: Membrane {ECO:0000305}; Single-pass membrane
  2164-CC       protein {ECO:0000305}.
  
  6003:CC   -!- SUBCELLULAR LOCATION: Secreted {ECO:0000305}.
  
  7039:CC   -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000305}; Lipid-anchor,
  7040-CC       GPI-anchor {ECO:0000305}. Note=In microneme/rhoptry complexes.
  7041-CC       {ECO:0000250}.
  
  7409:CC   -!- SUBCELLULAR LOCATION: Secreted {ECO:0000305}.
  
  8677:CC   -!- SUBCELLULAR LOCATION: Virion {ECO:0000269|PubMed:9499098}. Host
  8678-CC       endoplasmic reticulum-Golgi intermediate compartment
  8679-CC       {ECO:0000269|PubMed:15016891, ECO:0000269|PubMed:9499098}.
  
  12871:CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:P48349}.
  12872-CC       Cytoplasm {ECO:0000250|UniProtKB:P48349}. Note=Translocates from
  12873-CC       the cytosol to the nucleus when phosphorylated.
  12874-CC       {ECO:0000250|UniProtKB:P48349}.
  
  
  grep -A 6 -n -m 200 'CC   -!- SUBCELLULAR LOCATION.*(.*)'  /mnt/.../uniprot_sprot.dat
  
  
  1560049:CC   -!- SUBCELLULAR LOCATION: Secreted. Note=Dense core vesicles (DCV).
  
  2452012:CC   -!- SUBCELLULAR LOCATION: DNA-(apurinic or apyrimidinic site) lyase,
  2452013-CC       mitochondrial: Mitochondrion. Note=Translocation from the
  2452014-CC       cytoplasm to the mitochondria is mediated by ROS signaling and
  2452015-CC       cleavage mediated by granzyme A. Tom20-dependent translocated
  2452016-CC       mitochondrial APEX1 level is significantly increased after
  2452017-CC       genotoxic stress (By similarity). The cleaved APEX2 is only
  2452018-CC       detected in mitochondria. {ECO:0000250}.
  
  9243083:CC   -!- SUBCELLULAR LOCATION: Isoform Soluble copper chaperone CopA(Z):
  9243084-CC       Cytoplasm {ECO:0000250|UniProtKB:Q59385}.
  
  38197671:CC   -!- SUBCELLULAR LOCATION: E(rns) glycoprotein: Host cell membrane
  38197672-CC       {ECO:0000269|PubMed:28290554}; Peripheral membrane protein. Virion
  38197673-CC       membrane {ECO:0000269|PubMed:28290554}; Peripheral membrane
  38197674-CC       protein {ECO:0000305}. Note=The C-terminus membrane anchor of Erns
  38197675-CC       represents an amphipathic helix embedded in plane into the
  38197676-CC       membrane.
  
  4924705:CC   -!- SUBCELLULAR LOCATION: Note=(Microbial infection) In the presence
  4924706-CC       of M.tuberculosis EsxA-EsxB complex decreased amounts of B2M are
  4924707-CC       found on the cell surface (PubMed:25356553).
  4924708-CC       {ECO:0000269|PubMed:25356553}.
  
  02/18/2019
  For the DE line it is noted
  
  A block of DE lines may further contain multiple Includes: and/or Contains: sections and a separate field Flags: to indicate whether the protein sequence is a precursor or a fragment:
  
  At present this seems to be related to the answer. When I have the file correctly parsed, then I can check for a correspondence as verification.
  
  user1459: Thank you for asking this question. "Flag" is actually an obsolete notation which predates the introduction of proper evidence attribution in UniProtKB, and which escaped us in our efforts to update documentation to use the correct terminology. The correct  term would now be "Evidence", and the next version of the user manual will have this corrected (release 2019_06 due on July 3rd, 2019).
  Before the current way of evidencing annotations was introduced in UniProtKB, the following "non-experimental qualifiers" or "flags" were used: By similarity, Potential, Probable. Absence of such a flag would generally imply that the information is based on an experiment.
  When in doubt, please don't hesitate to contact the UniProt helpdesk. 
  
original_text: 1586: <p>In creating a parser for the UniProt flat file <code>uniprot_sprot.dat</code> (<a href="ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/" rel="nofollow noreferrer">directory</a>) in the <a href="https://www.uniprot.org/docs/userman.htm" rel="nofollow noreferrer">manual</a> for the section <code>SUBCELLULAR LOCATION</code> is listed </p>
  
  <blockquote>
    <p>The format of SUBCELLULAR LOCATION is:</p>
    
    <p>CC   -!- SUBCELLULAR LOCATION:(( Molecule:)?( Location.)+)?(
    Note=Free_text( <code>Flag</code>)?.)?</p>
    
    <p>Where:  </p>
    
    <ul>
    <li>Molecule: Isoform, chain or peptide name  </li>
    <li>Location = Subcellular_location( <code>Flag</code>)?(; Topology( <code>Flag</code>)?)?(; Orientation( <code>Flag</code>)?)? 
    
    <ul>
    <li>Subcellular_location: SL-line of subcell.txt ID-record </li>
    <li>Topology: SL-line of subcell.txt IT-record </li>
    <li>Orientation: SL-line of subcell.txt IO-record</li>
    </ul></li>
    </ul>
  </blockquote>
  
  <p>What does <code>Flag</code> mean?</p>
  
  <p>My best guess at present is that these are the text surrounded by parenthesis, e.g.</p>
  
  <pre><code> Note=Not associated with microtubules (PubMed:21558460).
  </code></pre>
  
  <p>but that does not help in understanding why it is named flag.</p>
  
  <p>While I can use my parser to verify this is correct when this section is working, it would be nicer to have a better understanding of what the word flag means in this context.</p>
  
  <p>I also checked the XML <a href="ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot.xsd" rel="nofollow noreferrer">schema</a> but no help there.</p>
  
  <hr>
  
  <p>Per request.</p>
  
  <p>More examples from file.</p>
  
  <p>These where gathered using grep. </p>
  
  <pre><code>grep -A 3 -n 'CC   -!- SUBCELLULAR LOCATION'  /mnt/.../uniprot_sprot.dat     
  </code></pre>
  
  <p><br></p>
  
  <pre><code>71:CC   -!- SUBCELLULAR LOCATION: Host membrane {ECO:0000305}; Single-pass
  72-CC       membrane protein {ECO:0000305}.
  
  2163:CC   -!- SUBCELLULAR LOCATION: Membrane {ECO:0000305}; Single-pass membrane
  2164-CC       protein {ECO:0000305}.
  
  6003:CC   -!- SUBCELLULAR LOCATION: Secreted {ECO:0000305}.
  
  7039:CC   -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000305}; Lipid-anchor,
  7040-CC       GPI-anchor {ECO:0000305}. Note=In microneme/rhoptry complexes.
  7041-CC       {ECO:0000250}.
  
  7409:CC   -!- SUBCELLULAR LOCATION: Secreted {ECO:0000305}.
  
  8677:CC   -!- SUBCELLULAR LOCATION: Virion {ECO:0000269|PubMed:9499098}. Host
  8678-CC       endoplasmic reticulum-Golgi intermediate compartment
  8679-CC       {ECO:0000269|PubMed:15016891, ECO:0000269|PubMed:9499098}.
  
  12871:CC   -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000250|UniProtKB:P48349}.
  12872-CC       Cytoplasm {ECO:0000250|UniProtKB:P48349}. Note=Translocates from
  12873-CC       the cytosol to the nucleus when phosphorylated.
  12874-CC       {ECO:0000250|UniProtKB:P48349}.
  </code></pre>
  
  <p><br></p>
  
  <pre><code>grep -A 6 -n -m 200 'CC   -!- SUBCELLULAR LOCATION.*(.*)'  /mnt/.../uniprot_sprot.dat
  </code></pre>
  
  <p><br></p>
  
  <pre><code>1560049:CC   -!- SUBCELLULAR LOCATION: Secreted. Note=Dense core vesicles (DCV).
  
  2452012:CC   -!- SUBCELLULAR LOCATION: DNA-(apurinic or apyrimidinic site) lyase,
  2452013-CC       mitochondrial: Mitochondrion. Note=Translocation from the
  2452014-CC       cytoplasm to the mitochondria is mediated by ROS signaling and
  2452015-CC       cleavage mediated by granzyme A. Tom20-dependent translocated
  2452016-CC       mitochondrial APEX1 level is significantly increased after
  2452017-CC       genotoxic stress (By similarity). The cleaved APEX2 is only
  2452018-CC       detected in mitochondria. {ECO:0000250}.
  
  9243083:CC   -!- SUBCELLULAR LOCATION: Isoform Soluble copper chaperone CopA(Z):
  9243084-CC       Cytoplasm {ECO:0000250|UniProtKB:Q59385}.
  
  38197671:CC   -!- SUBCELLULAR LOCATION: E(rns) glycoprotein: Host cell membrane
  38197672-CC       {ECO:0000269|PubMed:28290554}; Peripheral membrane protein. Virion
  38197673-CC       membrane {ECO:0000269|PubMed:28290554}; Peripheral membrane
  38197674-CC       protein {ECO:0000305}. Note=The C-terminus membrane anchor of Erns
  38197675-CC       represents an amphipathic helix embedded in plane into the
  38197676-CC       membrane.
  
  4924705:CC   -!- SUBCELLULAR LOCATION: Note=(Microbial infection) In the presence
  4924706-CC       of M.tuberculosis EsxA-EsxB complex decreased amounts of B2M are
  4924707-CC       found on the cell surface (PubMed:25356553).
  4924708-CC       {ECO:0000269|PubMed:25356553}.
  </code></pre>
  
  <p><strong>02/18/2019</strong></p>
  
  <p>For the DE line it is noted</p>
  
  <blockquote>
    <p>A block of DE lines may further contain multiple Includes: and/or Contains: sections and a separate field <code>Flags</code>: to indicate whether the protein sequence is a precursor or a fragment:</p>
  </blockquote>
  
  <p>At present this seems to be related to the answer. When I have the file correctly parsed, then I can check for a correspondence as verification.</p>
   1459: <p>Thank you for asking this question. "Flag" is actually an obsolete notation which predates the introduction of proper <a href="https://www.uniprot.org/help/evidences" rel="nofollow noreferrer">evidence attribution</a> in UniProtKB, and which escaped us in our efforts to update documentation to use the correct terminology. The correct  term would now be "Evidence", and the next version of the user manual will have this corrected (release 2019_06 due on July 3rd, 2019).</p>
  
  <p>Before the current way of evidencing annotations was introduced in UniProtKB, the following "non-experimental qualifiers" or "flags" were used: By similarity, Potential, Probable. Absence of such a flag would generally imply that the information is based on an experiment.</p>
  
  <p>When in doubt, please don't hesitate to contact the UniProt helpdesk. </p>
  