<commit_before><div class="help-sub-tab">
  <p>The rows in the following table describe the minimal components of a CIViC Evidence Item. Several Evidence Statements are synthesized at the Variant level into Variant Summaries but each Evidence Statement is directly linked to a single article in PubMed. <i>More specific guidelines about Evidence Item components can be found in additional help tabs.</i></p>

<h4>General Guidelines</h4>
<ul>
  <li>Evidence Statements should be:</li>
  <ul>
    <li>derived from primary literature sources (not review articles) whenever possible.</li>
    <li>as concise as possible while providing sufficient experiemental detail to interpret and evaluate the evidence (N values, statistics, etc).</li>
    <li>a single Predictive, Predisposing, Diagnostic or Prognostic assertion, not a combination.</li>
    <li>aimed at a general audience, avoiding field-specific acronyms and colloquialisms.</li>
  </ul>
  <li>Multiple, separate Evidence Items can be and often are derived from a single publication.</li>
  <li>Generally, assertions involving drugs should be classified as being of the Predictive Evidence Type.</li>
  <li>Evidence Ratings should be based on the strength of the specific assertion. Multiple assertions from the same publication can have different star ratings.</li>
</ul>
<h4>Evidence Attributes</h4>
    <table class="table table-striped table-condensed table-bordered">
     <colgroup>
        <col width="167.5"/>
        <col width="750"/>
        <col width="450"/>
        <col width="100"/>
     </colgroup>
      <tr>
        <th>Attribute</th>
        <th>Description</th>
        <th>Example</th>
        <th>Source</th>
      </tr>
      <tr>
        <td>Gene</td>
        <td>The symbol and ID of the gene implicated.</td>
        <td>ESR1 (Entrez ID: 2099)</td>
        <td>CIViC (Entrez)</td>
      </tr>
      <tr>
        <td>Variant</td>
        <td>Genomic event/mutation (Single nucleotide variant, Insertion/deletion, Gene fusion, Copy number variant, etc.) implicated.</td>
        <td>Y537S</td>
        <td>CIViC</td>
      </tr>
      <tr>
        <td>Evidence Statement</td>
        <td>Human readable interpretation. Free-form text summary of this event’s potential clinical interpretations. This interpretation is the synthesis of all other information about an event and its relevance to clinical action and should be the living product of active discussion.</td>
        <td>This study of 178 non-small cell lung cancer patients, the appearance of T790M mutation lead to resistance to gefitinib.</td>
        <td>CIViC</td>
      </tr>
      <tr>
        <td>Evidence Level</td>
        <td>The type of experiment from which the evidence is curated. From inferential, to proven association in clinical medicine. Refer to the additional documentation on evidence levels for definitions of the five levels allowed in CIViC: validated, clinical, pre-clinical, case study, and inferential.</td>
        <td>Level B - Clinical Evidence.</td>
        <td>CIViC</td>
      </tr>
      <tr>
        <td>Evidence Type</td>
        <td>Category of clinical action/relevance implicated by event. Refer to the additional documentation on evidence types for details on how to enter evidence of each of the four types: Predictive, Prognostic, Predisposing and Diagnostic. <i>See 'Evidence Type' tab for more information.</i></td>
        <td>Predictive - The variant is predictive of sensitivity or resistance to a therapeutic.</td>
        <td>CIViC</td>
      </tr>
      <tr>
        <td>Evidence Direction</td>
        <td>An indicator of whether the evidence statement supports or refutes the clinical significance of an event. <i>See 'Evidence Type' tab for more information.</i></td>
        <td>Supports - the evidence supports the clinical significance.</td>
        <td>CIViC</td>
      </tr>
      <tr>
      <tr>
        <td>Clinical Significance</td>
        <td>The association with diagnostic/prognostic end point or treatment. <i>See 'Evidence Type' tab for more information.</i></td>
        <td>Resistant or Non-response - mutation is associated with resistance to therapy.</td>
        <td>CIViC</td>
      </tr>
      <tr>
        <td>Variant Origin</td>
        <td>Presumed cellular origin of the Variant in samples from the literature citation where the clinical effect of this Variant is being evaluated.</td>
        <td>Somatic</td>
        <td>CIViC</td>
      </tr>
      <tr>
        <td>Disease</td>
        <td>Specific disease or disease subtype that is associated with this event and its clinical implication. Links directly to Disease Ontology.</td>
        <td>Estrogen-receptor positive breast cancer (DOID: 0060075).</td>
        <td>CIViC (Disease Ontology)</td>
      </tr>
      <tr>
        <td>Drug</td>
        <td>For predictive evidence, indicates the therapy for which sensitivity or resistance is indicated (With PubChem ID if available).</td>
        <td>Tamoxifen, Raloxifene (PubChem CIDs: 2733526, 5053).</td>
        <td>CIViC (PubChem)</td>
      </tr>
      <tr>
        <td>Drug Interaction Type</td>
        <td>For predictive evidence involving more than one drug, specifies the relationship between these drugs by indicating whether the drugs are Subtitutes for each other or are used in Sequential or Combination treatments.</td>
        <td>Substitutes - The drugs listed are often considered to be of the same family, or behave similarly in a treatment setting.</td>
        <td>CIViC</td>
      <tr>
        <td>Citation</td>
        <td>Publication where the event was described/explored automatically generated from curator-provided PubMed ID and links to internal CIViC publication page showing all Evidence Items from the publication.</td>
        <td><NAME> al., 2013, Nat. Genet. (PMID: 24185512)</td>
        <td>CIViC (PubMed)</td>
      </tr>
      <tr>
        <td>PubMed ID</td>
        <td>PubMed ID for publication where the event was described/explored with direct link to PubMed.</td>
        <td>24185512</td>
        <td>CIViC (PubMed)</td>
      </tr>
      <tr>
        <td>Evidence Rating</td>
        <td>A rating on a 5-star scale, portraying the curators trust in the experiments from which the evidence is curated. Refer to the additional documentation on evidence ratings for guidance on how to score an evidence item.</td>
        <td>5-stars - Strong, well supported evidence from a lab or journal with respected academic standing. Experiments are well controlled, and results are clean and reproducible across multiple replicates.</td>
        <td>CIViC</td>
      </tr>
    </table>

</div>
<commit_msg>tweaked help copy referring to pubchem IDs<commit_after><div class="help-sub-tab">
  <p>The rows in the following table describe the minimal components of a CIViC Evidence Item. Several Evidence Statements are synthesized at the Variant level into Variant Summaries but each Evidence Statement is directly linked to a single article in PubMed. <i>More specific guidelines about Evidence Item components can be found in additional help tabs.</i></p>

<h4>General Guidelines</h4>
<ul>
  <li>Evidence Statements should be:</li>
  <ul>
    <li>derived from primary literature sources (not review articles) whenever possible.</li>
    <li>as concise as possible while providing sufficient experiemental detail to interpret and evaluate the evidence (N values, statistics, etc).</li>
    <li>a single Predictive, Predisposing, Diagnostic or Prognostic assertion, not a combination.</li>
    <li>aimed at a general audience, avoiding field-specific acronyms and colloquialisms.</li>
  </ul>
  <li>Multiple, separate Evidence Items can be and often are derived from a single publication.</li>
  <li>Generally, assertions involving drugs should be classified as being of the Predictive Evidence Type.</li>
  <li>Evidence Ratings should be based on the strength of the specific assertion. Multiple assertions from the same publication can have different star ratings.</li>
</ul>
<h4>Evidence Attributes</h4>
    <table class="table table-striped table-condensed table-bordered">
     <colgroup>
        <col width="167.5"/>
        <col width="750"/>
        <col width="450"/>
        <col width="100"/>
     </colgroup>
      <tr>
        <th>Attribute</th>
        <th>Description</th>
        <th>Example</th>
        <th>Source</th>
      </tr>
      <tr>
        <td>Gene</td>
        <td>The symbol and ID of the gene implicated.</td>
        <td>ESR1 (Entrez ID: 2099)</td>
        <td>CIViC (Entrez)</td>
      </tr>
      <tr>
        <td>Variant</td>
        <td>Genomic event/mutation (Single nucleotide variant, Insertion/deletion, Gene fusion, Copy number variant, etc.) implicated.</td>
        <td>Y537S</td>
        <td>CIViC</td>
      </tr>
      <tr>
        <td>Evidence Statement</td>
        <td>Human readable interpretation. Free-form text summary of this event’s potential clinical interpretations. This interpretation is the synthesis of all other information about an event and its relevance to clinical action and should be the living product of active discussion.</td>
        <td>This study of 178 non-small cell lung cancer patients, the appearance of T790M mutation lead to resistance to gefitinib.</td>
        <td>CIViC</td>
      </tr>
      <tr>
        <td>Evidence Level</td>
        <td>The type of experiment from which the evidence is curated. From inferential, to proven association in clinical medicine. Refer to the additional documentation on evidence levels for definitions of the five levels allowed in CIViC: validated, clinical, pre-clinical, case study, and inferential.</td>
        <td>Level B - Clinical Evidence.</td>
        <td>CIViC</td>
      </tr>
      <tr>
        <td>Evidence Type</td>
        <td>Category of clinical action/relevance implicated by event. Refer to the additional documentation on evidence types for details on how to enter evidence of each of the four types: Predictive, Prognostic, Predisposing and Diagnostic. <i>See 'Evidence Type' tab for more information.</i></td>
        <td>Predictive - The variant is predictive of sensitivity or resistance to a therapeutic.</td>
        <td>CIViC</td>
      </tr>
      <tr>
        <td>Evidence Direction</td>
        <td>An indicator of whether the evidence statement supports or refutes the clinical significance of an event. <i>See 'Evidence Type' tab for more information.</i></td>
        <td>Supports - the evidence supports the clinical significance.</td>
        <td>CIViC</td>
      </tr>
      <tr>
      <tr>
        <td>Clinical Significance</td>
        <td>The association with diagnostic/prognostic end point or treatment. <i>See 'Evidence Type' tab for more information.</i></td>
        <td>Resistant or Non-response - mutation is associated with resistance to therapy.</td>
        <td>CIViC</td>
      </tr>
      <tr>
        <td>Variant Origin</td>
        <td>Presumed cellular origin of the Variant in samples from the literature citation where the clinical effect of this Variant is being evaluated.</td>
        <td>Somatic</td>
        <td>CIViC</td>
      </tr>
      <tr>
        <td>Disease</td>
        <td>Specific disease or disease subtype that is associated with this event and its clinical implication. Links directly to Disease Ontology.</td>
        <td>Estrogen-receptor positive breast cancer (DOID: 0060075).</td>
        <td>CIViC (Disease Ontology)</td>
      </tr>
      <tr>
        <td>Drug</td>
        <td>For predictive evidence, indicates the therapy for which sensitivity or resistance is indicated (With PubChem ID or ASCO Abstract ID if available).</td>
        <td>Tamoxifen, Raloxifene (PubChem CIDs: 2733526, 5053).</td>
        <td>CIViC (PubChem/ASCO Abstract ID)</td>
      </tr>
      <tr>
        <td>Drug Interaction Type</td>
        <td>For predictive evidence involving more than one drug, specifies the relationship between these drugs by indicating whether the drugs are Subtitutes for each other or are used in Sequential or Combination treatments.</td>
        <td>Substitutes - The drugs listed are often considered to be of the same family, or behave similarly in a treatment setting.</td>
        <td>CIViC</td>
      <tr>
        <td>Citation</td>
        <td>Publication where the event was described/explored automatically generated from curator-provided PubMed ID and links to internal CIViC publication page showing all Evidence Items from the publication.</td>
        <td>Toy et al., 2013, Nat. Genet. (PMID: 24185512)</td>
        <td>CIViC (PubMed)</td>
      </tr>
      <tr>
        <td>PubMed ID</td>
        <td>PubMed ID for publication where the event was described/explored with direct link to PubMed.</td>
        <td>24185512</td>
        <td>CIViC (PubMed)</td>
      </tr>
      <tr>
        <td>Evidence Rating</td>
        <td>A rating on a 5-star scale, portraying the curators trust in the experiments from which the evidence is curated. Refer to the additional documentation on evidence ratings for guidance on how to score an evidence item.</td>
        <td>5-stars - Strong, well supported evidence from a lab or journal with respected academic standing. Experiments are well controlled, and results are clean and reproducible across multiple replicates.</td>
        <td>CIViC</td>
      </tr>
    </table>

</div>

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