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Anchor | Evidence Codes | Evidence Codes | Evidence CodesEvidence codes qualify the assertions with respect to the association of a gene to a disease or compound term by telling how the assertions were made (e.g., through inference or experimental data). The curators may have identified the means by which an assertion using the extracted sentence, alone, or through careful reading of the abstract from which the sentence originated. These codes follow the suggestions of Karp et al. for ontologies used in pathway and genome databases. The Evidence Code associated with a specific gene-disease or gene-compound pair is found in the text contents of the XMLEvidenceCode element and is the EvidenceCode attribute of the caBIO Evidence Code class ,
Evidence Code Description
 No Evidence Code was assigned because the sentence did not contain the expected gene-disease or gene-compound association evidence. Anchor | Role | Role | Role Code and Role Detail SimilaritiesThe Cancer Gene Index Role Codes and Role Details are derived from NCI Role Codes. Both describe the semantic associations between gene concept and either a disease or compound concept (i.e., concept pairs). Whereas the Evidence Codes describe how the association was inferred or the type of experiment upon which the inference was made, Role Codes and Role Details give information about the actual gene-disease or gene-compound association. Multiple Role Codes and Role Details can be used for the same sentence.
Anchor | Role Codes | Role Codes | Role CodesGene-Disease and Gene-Compound Role Codes most often describe that a gene is associated with a disease or compound (e.g.,
PrimaryNCIRoleCode element and is the role attribute of the caBIO GeneDiseaseAssociation and GeneAgentAssociation classes,
Role Details
OtherRole element and is, like Role Codes, the role attribute of the caBIO GeneDiseaseAssociation and GeneAgentAssociation classes.Gene-Disease Role Details
Indicators | Indicators | Cell Line and Negation IndicatorsThe binary indicatorsyes or no were set for cell line and negation annotations of each gene-disease and gene-compound association. Anchor | cell line indicators | cell line indicators | Cell line indicators denote whether the evidence came from a cell line (yes ) or other source, such a human subject, animal model, or primary cells (no ). The cell line indicator is the text contents of the XML CelllineIndicator element and the celllineStatus attribute of the caBIO Evidence class. Anchor | negation indicators | negation indicators | Negation indicators specify whether the evidence actually described a lack of association between the candidate binary concept pair (yes ), or whether there was a true relationship between them (no ). The curators may have deduced the negation indicator by the extracted sentence, alone, or through careful reading of the abstract from which the sentence originated. Occasionally, the curators did not set a negation indicator (- ). The negation indicator is the text contents of the XML NegationIndicator element and the negationStatus attribute of the caBIO Evidence class. Anchor | status flags | status flags | Status FlagsThe curators set flags to denote the state of annotations of a gene term or of a particular sentence. Anchor | gene status flags | gene status flags | Gene Status FlagsGene Status Flags describe whether annotations for all of the sentences for a given gene term are complete and whether the gene term has been withdrawn from EntrezGene. All low frequency sentence count genes were finished, whereas some high frequency sentence count genes were not. The status of a specific gene is found in the text contents of the XML Anchor | Gene Status Flags | Gene Status Flags |
Anchor | sentence status flags | sentence status flags | Sentence Status FlagsUnlike gene status flags, which can cover many sentences associated with a single gene, Sentence Status Flags describe the curator's findings for a specific sentence. Sentences can be true positives, false positives, unclear, or redundant. The status of a specific gene is found in the text contents of the XML Anchor | Sentence Status Flags | Sentence Status Flags |
Anchor | comments | comments | CommentsOften, the expert curators made free-text comments on records within the Gene-Disease or Gene-Compound databases. Comments included, but were not limited to, notations of genetic anomalies (e.g., loss of heterozygosity, polymorphisms, or aberrant methylation), additional disease information, name of the non-human organism from which the experimental data were collected, information on the cell line or other notable reagents used in the execution of the experiment, and other miscellaneous information. Any comments on a sentence are found in the text contents of the XMLComments element and the comment attribute of the caBIO Evidence class.
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