Assertions vs Evidence: Key Differences

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You 01:23 AM

How does an assertion differ from an evidence item?

CIViC Bot 01:23 AM

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search_docs(query: "assertion vs evidence item CIViC difference 'assertion' 'evidence item' CIViC ReadTheDocs")

Tool Result 01:23 AM

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                [
  {
    "link": "https://civic.readthedocs.io/en/latest/model/assertions.html",
    "title": "assertions",
    "contents": "Assertions — CIViC documentation About CIViC CIViC Knowledge Model Evidence Items Assertions Assertions Overview Fields Shared with Evidence Associated Phenotypes NCCN Guideline FDA Companion Test Summary and Description Features Molecular Profiles Variants Genes Fusions Factors Variant Groups Sources Curating CIViC User Interface and Data CIViC API Get Help CIViC Docs » CIViC Knowledge Model » Assertions View page source Assertions¶ An assertion classifies the clinical significance of a variant-disease associate under recognized guidelines. This section of the documentation details the knowledge model that CIViC uses for representing assertions. Each page roughly corresponds to a field in the Assertion schema. Note that Assertions share several key fields with Evidence Items, listed on the Shared Fields page along with notes regarding differences in the meaning of those fields between the two entities. Assertions Overview Fields Shared with Evidence Associated Phenotypes Curating Associated Phenotypes NCCN Guideline Understanding NCCN Guidelines Curating NCCN Guidelines FDA Companion Test Understanding FDA Companion Tests Curating FDA Companion Tests Summary and Description Next Previous Visit the CIViC resource at civicdb.org. Disclaimer: CIViC is intended for purely research purposes. It should not be used for emergencies or medical or professional advice. CIViC by The McDonnell Genome Institute at Washington University School of Medicine is licensed under a Creative Commons Public Domain Dedication (CC0 1.0 Universal) jQuery(function () { SphinxRtdTheme.Navigation.enable(true); });",
    "document_type": "read_the_docs"
  },
  {
    "link": "https://civic.readthedocs.io/en/latest/model/assertions/overview.html",
    "title": "overview",
    "contents": "Assertions Overview — CIViC documentation About CIViC CIViC Knowledge Model Evidence Items Assertions Assertions Overview Fields Shared with Evidence Associated Phenotypes NCCN Guideline FDA Companion Test Summary and Description Features Molecular Profiles Variants Genes Fusions Factors Variant Groups Sources Curating CIViC User Interface and Data CIViC API Get Help CIViC Docs » CIViC Knowledge Model » Assertions » Assertions Overview View page source Assertions Overview¶ An assertion classifies the clinical significance of a variant-disease association under recognized guidelines (see AMP Classification, NCCN Guidelines, for more). Figure 1: Assertion Attributes and Associations The CIViC Assertion (AID) summarizes a collection of Evidence Items (EIDs) that covers predictive/therapeutic, diagnostic, prognostic, predisposing or oncogenic information for a molecular profile (variant) in a specific cancer context (Figure 1). Functional Assertions are not currently supported. In general, an Assertion of a certain Type (e.g. Diagnostic) will be supported by a collection of Evidence Items (EIDs) of the same type, but Functional EIDs may be used to support Assertions of other types. The collection of EIDs associated with an Assertion should cover the important clinically relevant findings for the variant in the context of the specific cancer (and drug entity for Predictive Assertions). Assertion summaries mention NCCN or other practice guidelines related to the variant, as well as FDA drug approvals. In place of the curator assigned star rating found in CIViC Evidence Items, CIViC Assertions utilize widely adopted, published guidelines for variant tiering and pathogenicity/oncogenicity assessment, which are detailed below. CIViC Assertions are the primary entity that make up CIViC submissions to ClinVar. CIViC currently has two main types of Assertions: those based on variants of primarily somatic origin (predictive/therapeutic, prognostic, diagnostic, and oncogenic) and those based on variants of primarily germline origin (predisposing). When the number and quality of Predictive, Prognostic, Diagnostic, Predisposing or Oncogenic Evidence Items (EIDs) in CIViC sufficiently cover what is known for a particular Molecular Profile and cancer type, then a corresponding assertion may be created in CIViC. Next Previous Visit the CIViC resource at civicdb.org. Disclaimer: CIViC is intended for purely research purposes. It should not be used for emergencies or medical or professional advice. CIViC by The McDonnell Genome Institute at Washington University School of Medicine is licensed under a Creative Commons Public Domain Dedication (CC0 1.0 Universal) jQuery(function () { SphinxRtdTheme.Navigation.enable(true); });",
    "document_type": "read_the_docs"
  },
  {
    "link": "https://civic.readthedocs.io/en/latest/api/v1/assertions.html",
    "title": "assertions",
    "contents": "Assertions — CIViC documentation Contents: About CIViC Using CIViC Curating CIViC CIViC Knowledge Model CIViC API V2 API V1 API (deprecated) Endpoint Types Genes Variants Evidence Items Variant Groups Assertions Get a list of assertions Get details for a specific assertion Linking Metadata Throttling Constructing Add Evidence URLs Get Help CIViC Docs » CIViC API » Assertions View page source Assertions¶ The assertions endpoint allows users to enumerate all of the assertions present in CIViC as well as retrieve more detailed information on a specific assertion. This is the endpoint that should be used to obtain a complete listing of every assertion in CIViC. Get a list of assertions¶ This endpoint returns a listing of assertions in CIViC. This index style endpoint is paginated by default. You can use the count and page parameters or the previous and next links to iterate through all the assertions. HTTP Request Format GET https://civicdb.org/api/assertions Query Parameters Parameter Default Description page 1 Which page of results to return count 25 How many assertions to return on a single page Example Request curl https://civicdb.org/api/assertions?count=1 Example Response Expecting value: line 1 column 1 (char 0) Get details for a specific assertion¶ This endpoint retrieves details about a specific assertion, given its internal CIViC id. HTTP Request Format GET https://civicdb.org/api/assertions/:id Example Request curl https://civicdb.org/api/assertions/9 Example Response Expecting value: line 1 column 1 (char 0) Next Previous Visit the CIViC resource at civicdb.org. Disclaimer: CIViC is intended for purely research purposes. It should not be used for emergencies or medical or professional advice. CIViC by The McDonnell Genome Institute at Washington University School of Medicine is licensed under a Creative Commons Public Domain Dedication (CC0 1.0 Universal) jQuery(function () { SphinxRtdTheme.Navigation.enable(true); });",
    "document_type": "read_the_docs"
  },
  {
    "link": "https://civic.readthedocs.io/en/latest/model/assertions/shared_fields.html",
    "title": "shared_fields",
    "contents": "Fields Shared with Evidence — CIViC documentation About CIViC CIViC Knowledge Model Evidence Items Assertions Assertions Overview Fields Shared with Evidence Associated Phenotypes NCCN Guideline FDA Companion Test Summary and Description Features Molecular Profiles Variants Genes Fusions Factors Variant Groups Sources Curating CIViC User Interface and Data CIViC API Get Help CIViC Docs » CIViC Knowledge Model » Assertions » Fields Shared with Evidence View page source Fields Shared with Evidence¶ Assertions share several fields with evidence, which for the most part can be understood and curated in the same manner. Please review the evidence documentation for these fields, and the notes below on any nuances in interpretation or curation between entity’s fields. Shared Field Evidence Documentation Notes Gene Gene Field Molecular Profile Molecular Profile Field Origin Origin Field Disease Disease Field In some cases, several evidence items with non-identical but highly related disease terms may be incorporated into a single assertion. In this case, choose the most general disease category that includes all of the evidence diseases. Type Type Field Direction Direction Field Significance Significance Field Next Previous Visit the CIViC resource at civicdb.org. Disclaimer: CIViC is intended for purely research purposes. It should not be used for emergencies or medical or professional advice. CIViC by The McDonnell Genome Institute at Washington University School of Medicine is licensed under a Creative Commons Public Domain Dedication (CC0 1.0 Universal) jQuery(function () { SphinxRtdTheme.Navigation.enable(true); });",
    "document_type": "read_the_docs"
  }
]

CIViC Bot 01:23 AM

Tool Call

search_docs(query: "evidence items CIViC documentation 'Evidence Items' 'overview' 'evidence item' ReadTheDocs CIViC model evidence items overview fields")

Tool Result 01:23 AM

Tool Result

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                [
  {
    "link": "https://civic.readthedocs.io/en/latest/model/evidence.html",
    "title": "evidence",
    "contents": "Evidence Items — CIViC documentation About CIViC CIViC Knowledge Model Evidence Items Evidence Overview Gene Molecular Profile Statement Evidence Level Type Direction Significance Origin Disease Therapy Associated Phenotype Source Clinical Trial Evidence Rating Assertions Features Molecular Profiles Variants Genes Fusions Factors Variant Groups Sources Curating CIViC User Interface and Data CIViC API Get Help CIViC Docs » CIViC Knowledge Model » Evidence Items View page source Evidence Items¶ At the heart of CIViC is the clinical evidence statement. The clinical evidence statement is a piece of information that has been manually curated from trustable medical literature about a molecular profile (variant) or genomic ‘event’ that has implications for protein function, oncogenicity, cancer predisposition, diagnosis (aka molecular classification), prognosis, or predictive response to therapy. For example, “Patients with BRAF V600 mutations respond well to the drug dabrafenib”. A molecular profile is comprised of one or more variant(s) which may be a single nucleotide substitution, a small insertion or deletion, an RNA gene fusion, a chromosomal rearrangement, an RNA expression pattern (e.g. over-expression), etc. Each clinical evidence statement corresponds to a single citable publication. Evidence Items follow a structured knowledge model with required fields: Molecular Profile Name (Gene/Variant), Source, Variant Origin, Disease, Evidence Statement, Evidence Type, Evidence Level, Evidence Direction, Significance, and Trust Rating) with additional optional fields (Associated Phenotypes, etc). For some Evidence Types, additional required or optional fields become available (e.g., Predictive Evidence Types require a Therapy/Drug Name). Evidence Overview Gene Curating Genes Molecular Profile Statement Understanding Evidence Statements Curating Evidence Statements Evidence Level Understanding Evidence Levels Curating Levels Type Understanding Evidence Types Direction Understanding Evidence Direction Curating Evidence Direction Significance Understanding Significance Origin Understanding Variant Origin Curating Variant Origin Disease Curating Diseases Therapy Curating Therapies Associated Phenotype Curating Associated Phenotypes Source Understanding Source Curating Source Clinical Trial Evidence Rating Understanding Evidence Ratings Curating Evidence Ratings Next Previous Visit the CIViC resource at civicdb.org. Disclaimer: CIViC is intended for purely research purposes. It should not be used for emergencies or medical or professional advice. CIViC by The McDonnell Genome Institute at Washington University School of Medicine is licensed under a Creative Commons Public Domain Dedication (CC0 1.0 Universal) jQuery(function () { SphinxRtdTheme.Navigation.enable(true); });",
    "document_type": "read_the_docs"
  },
  {
    "link": "https://civic.readthedocs.io/en/latest/api/v1/evidence.html",
    "title": "evidence",
    "contents": "Evidence Items — CIViC documentation Contents: About CIViC Using CIViC Curating CIViC CIViC Knowledge Model CIViC API V2 API V1 API (deprecated) Endpoint Types Genes Variants Evidence Items Get a list of evidence items Get details for a specific evidence item Variant Groups Assertions Linking Metadata Throttling Constructing Add Evidence URLs Get Help CIViC Docs » CIViC API » Evidence Items View page source Evidence Items¶ The evidence items endpoint allows users to enumerate all of the evidence items present in CIViC as well as retrieve more detailed information on a specific evidence item. This is the endpoint that should be used to obtain a complete listing of every evidence item in CIViC. Get a list of evidence items¶ This endpoint returns a listing of evidence items in CIViC. This index style endpoint is paginated by default. You can use the count and page parameters or the previous and next links to iterate through all the evidence items. HTTP Request Format GET https://civicdb.org/api/evidence_items Query Parameters Parameter Default Description page 1 Which page of results to return count 25 How many evidence items to return on a single page Example Request curl https://civicdb.org/api/evidence_items?count=1 Example Response Expecting value: line 1 column 1 (char 0) Get details for a specific evidence item¶ This endpoint retrieves details about a specific evidence item, given its internal CIViC id. HTTP Request Format GET https://civicdb.org/api/evidence_items/:id Example Request curl https://civicdb.org/api/evidence_items/512 Example Response Expecting value: line 1 column 1 (char 0) Next Previous Visit the CIViC resource at civicdb.org. Disclaimer: CIViC is intended for purely research purposes. It should not be used for emergencies or medical or professional advice. CIViC by The McDonnell Genome Institute at Washington University School of Medicine is licensed under a Creative Commons Public Domain Dedication (CC0 1.0 Universal) jQuery(function () { SphinxRtdTheme.Navigation.enable(true); });",
    "document_type": "read_the_docs"
  },
  {
    "link": "https://civic.readthedocs.io/en/latest/model/evidence/overview.html",
    "title": "overview",
    "contents": "Evidence Overview — CIViC documentation About CIViC CIViC Knowledge Model Evidence Items Evidence Overview Gene Molecular Profile Statement Evidence Level Type Direction Significance Origin Disease Therapy Associated Phenotype Source Clinical Trial Evidence Rating Assertions Features Molecular Profiles Variants Genes Fusions Factors Variant Groups Sources Curating CIViC User Interface and Data CIViC API Get Help CIViC Docs » CIViC Knowledge Model » Evidence Items » Evidence Overview View page source Evidence Overview¶ The following figure shows the attributes of a CIViC Evidence Item, and the options or values available for each. Figure 1: Evidence Item Attributes and Associations The rows in the following table describe the minimal components of a CIViC Evidence Item. Several Evidence Statements are synthesized at the Molecular Profile (Variant) level into a Molecular Profile Description. However, each Evidence Statement is directly linked to a single article in PubMed or ASCO/ASH abstract. More specific guidelines about Evidence Item components can be found in the additional sections outlined in the table of contents. Evidence Attributes Attribute Description Example Source Molecular Profile Gene and Genomic event(s)/mutation(s) (e.g., Single nucleotide variant, Insertion/deletion, Gene fusion, Copy number variant, etc.) implicated. May be a simple comprised of a single variant or a more complex combination of variants. ESR1 Y537S CIViC Statement Human readable interpretation. Free-form text summary of this molecular profile’s potential clinical interpretations. This interpretation is the synthesis of all other information about the alteration(s) and its clinical relevance and should be the living product of active discussion. In this study of 178 non-small cell lung cancer patients, the appearance of EGFR T790M mutation led to resistance to gefitinib. CIViC Evidence Level 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. Level B - Clinical Evidence. CIViC Type 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 six types: Predictive, Prognostic, Diagnostic, Predisposing, Oncogenic and Functional. See ‘Evidence Type’ tab for more information. Predictive - The molecular profile (one or more variants) is predictive of sensitivity or resistance to a therapeutic. CIViC Direction An indicator of whether the evidence statement supports or refutes the significance of an event. See ‘Evidence Type’ tab for more information. Supports - the evidence supports the significance. CIViC Significance The impact of the molecular profile (one or more variants) for predictive, prognostic, diagnostic, oncogenic or functional evidence types. See ‘Evidence Type’ tab for more information. Resistant or Non-response - mutation is associated with resistance to therapy. CIViC Origin Presumed cellular origin of the Variant in samples from the literature citation where the effect of this Variant is being evaluated. Somatic CIViC Disease Specific disease or disease subtype that is associated with this event and its clinical implication. Links directly to Disease Ontology. Estrogen-receptor positive breast cancer (DOID: 0060075). CIViC (Disease Ontology) Associated Phenotype Specific phenotypes associated with the evidence statement. Pancreatic cysts (HP:0001737). The Human Phenotype Ontology (HPO) Therapy For predictive evidence, indicates the therapy for which sensitivity or resistance is indicated (With NCIt ID if available). Tamoxifen, Raloxifene (NCIt IDs: C62078, C62078). CIViC (NCIt) Therapy Interaction Type For predictive evidence involving more than one Therapy, specifies the relationship between the therapies (usually drugs) by indicating whether they are Subtitutes for each other or are used in Sequential or Combination treatments. Substitutes - The therapies listed are often considered to be of the same family, or behave similarly in a treatment setting. CIViC Citation 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. Toy et al., 2013, Nat. Genet. (PMID: 24185512) CIViC (PubMed) PubMed ID PubMed ID for publication where the event was described/explored with direct link to PubMed. 24185512 CIViC (PubMed) Clinical Trial Clinical trial associated with the evidence item. NCT01154140 ClinicalTrials.gov Evidence Rating 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 trust ratings for guidance on how to score an evidence item. 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. CIViC Next Previous Visit the CIViC resource at civicdb.org. Disclaimer: CIViC is intended for purely research purposes. It should not be used for emergencies or medical or professional advice. CIViC by The McDonnell Genome Institute at Washington University School of Medicine is licensed under a Creative Commons Public Domain Dedication (CC0 1.0 Universal) jQuery(function () { SphinxRtdTheme.Navigation.enable(true); });",
    "document_type": "read_the_docs"
  },
  {
    "link": "https://civic.readthedocs.io/en/latest/model.html",
    "title": "model",
    "contents": "CIViC Knowledge Model — CIViC documentation About CIViC CIViC Knowledge Model Evidence Items Assertions Features Molecular Profiles Variants Genes Fusions Factors Variant Groups Sources Curating CIViC User Interface and Data CIViC API Get Help CIViC Docs » CIViC Knowledge Model View page source CIViC Knowledge Model¶ This section describes the details of the knowledge model that CIViC uses to organize variant interpretations, evidence, assertions and associated information about therapies, disease type, etc. Each major entity is detailed in the sections below, with each attribute of that entity detailed within its own page (roughly). Evidence Items Evidence Overview Gene Molecular Profile Statement Evidence Level Type Direction Significance Origin Disease Therapy Associated Phenotype Source Clinical Trial Evidence Rating Assertions Assertions Overview Fields Shared with Evidence Associated Phenotypes NCCN Guideline FDA Companion Test Summary and Description Features Overview of Features Feature-Variant Pairs Browsing Features Molecular Profiles Molecular Profiles Overview Name Aliases Description Molecular Profile Score Variants Variants Overview Name Aliases My Variant Info Types Coordinates HGVS Expressions ClinVar IDs Genes Gene Name Summary MyGene.info Fusions Fusion Variants Fusion Feature page Fusion Variant Page Fusion Variant Coordinates Factors The Factor Page View The Factor Variant Page Browsing Factors Variant Groups Summary Sources Source Types Next Previous Visit the CIViC resource at civicdb.org. Disclaimer: CIViC is intended for purely research purposes. It should not be used for emergencies or medical or professional advice. CIViC by The McDonnell Genome Institute at Washington University School of Medicine is licensed under a Creative Commons Public Domain Dedication (CC0 1.0 Universal) jQuery(function () { SphinxRtdTheme.Navigation.enable(true); });",
    "document_type": "read_the_docs"
  }
]

CIViC Bot 01:23 AM

Short answer

An Evidence Item (EID) is a single, structured clinical evidence statement curated from one publication about a molecular profile (variant) and its clinical implication.

Excerpt: “At the heart of CIViC is the clinical evidence statement. … Each clinical evidence statement corresponds to a single citable publication.” [ 1 ]
An Assertion (AID) is an aggregated, higher-level classification that summarizes a collection of Evidence Items for the same molecular profile in a specific disease context and assigns clinical significance according to established guidelines (AMP/NCCN/FDA, etc.).

Excerpt: “An assertion classifies the clinical significance of a variant-disease association under recognized guidelines… The CIViC Assertion (AID) summarizes a collection of Evidence Items (EIDs) that covers predictive/therapeutic, diagnostic, prognostic, predisposing or oncogenic information for a molecular profile (variant) in a specific cancer context.” [ 2 ]

Key practical differences

Scope
- Evidence Item: single publication / single evidence statement about a molecular profile. [ 1 ]
- Assertion: synthesizes multiple Evidence Items to provide an overall classification for that molecular profile in a disease (and drug, for predictive assertions). [ 2 ]
Purpose
- Evidence Item: capture and rate trust in the primary experimental/clinical observation (includes curator trust rating/stars).
- Assertion: provide guideline-based clinical classification/tiering or pathogenicity/oncogenicity calls (used for ClinVar submissions) rather than curator star ratings. “In place of the curator assigned star rating found in CIViC Evidence Items, CIViC Assertions utilize widely adopted, published guidelines for variant tiering and pathogenicity/oncogenicity assessment.” [ 2 ]
Granularity and curation rules
- Evidence Items are linked 1:1 to citations and specific experiment/observation details (level, type, direction, significance, origin, disease, therapy, etc.). [ 1 ]
- Assertions may combine several related evidence items (including ones with closely related disease terms) into a single, summarized disease term or classification: “In some cases, several evidence items with non-identical but highly related disease terms may be incorporated into a single assertion. In this case, choose the most general disease category that includes all of the evidence diseases.” [ 3 ]

When to create an Assertion

An Assertion is created when the number and quality of relevant Predictive/Prognostic/Diagnostic/Predisposing/Oncogenic Evidence Items sufficiently cover what is known for a given molecular profile and cancer type; the Assertion then summarizes those EIDs and applies guideline-based classification. [ 2 ]

Bottom line

Evidence Items = individual, citation-linked clinical statements (the building blocks).
Assertions = curated synthesis/classification of those building blocks into a guideline-based clinical interpretation for a molecular profile in a defined disease context.

Sources

You 03:24 AM

What evidence types does CIViC support?

CIViC Bot 03:24 AM

Tool Call

search_docs(query: "CIViC evidence types Predictive Prognostic Diagnostic Predisposing Oncogenic Functional 'Evidence Type' ReadTheDocs civic model evidence types")

Tool Result 03:24 AM

Tool Result

Click to expand


                [
  {
    "link": "https://civic.readthedocs.io/en/latest/model/evidence/type.html",
    "title": "type",
    "contents": "Type — CIViC documentation About CIViC CIViC Knowledge Model Evidence Items Evidence Overview Gene Molecular Profile Statement Evidence Level Type Understanding Evidence Types Direction Significance Origin Disease Therapy Associated Phenotype Source Clinical Trial Evidence Rating Assertions Features Molecular Profiles Variants Genes Fusions Factors Variant Groups Sources Curating CIViC User Interface and Data CIViC API Get Help CIViC Docs » CIViC Knowledge Model » Evidence Items » Type View page source Type¶ The Evidence Type refers to the type of clinical (or biological) association described by the Evidence Item’s clinical summary. Understanding Evidence Types¶ Six Evidence Types are currently supported: Predictive (i.e. Therapeutic), Diagnostic, Prognostic, Predisposing, Oncogenic, and Functional. Each Evidence Type describes the clinical or biological effect a Molecular Profile (MP) has on the following: therapeutic response (Predictive), determining a patient’s diagnosis or disease subtype (Diagnostic), predicting disease progression or patient survival (Prognostic), disease susceptibility (Predisposing), or biological alterations relevant to a cancer phenotype (Oncogenic) or protein function (Functional). Selecting an Evidence Type has implications on available selections for Significance, which are detailed on the Evidence Significance page. Type Icon Definition Diagnostic Evidence pertains to a variant’s impact on patient diagnosis (cancer subtype) Predictive Evidence pertains to a variant’s effect on therapeutic response Prognostic Evidence pertains to a variant’s impact on disease progression, severity, or patient survival. Predisposing Evidence pertains to a germline Molecular Profile’s role in conferring susceptibility to disease (including pathogenicity evaluations) Oncogenic Evidence pertains to a somatic variant’s involvement in tumor pathogenesis as described by the Hallmarks of Cancer. Functional Evidence pertains to a variant that alters biological function from the reference state. Extensive documentation for curating Evidence types is provided on the Curating Evidence page. Be sure to closly study the examples for each type. Next Previous Visit the CIViC resource at civicdb.org. Disclaimer: CIViC is intended for purely research purposes. It should not be used for emergencies or medical or professional advice. CIViC by The McDonnell Genome Institute at Washington University School of Medicine is licensed under a Creative Commons Public Domain Dedication (CC0 1.0 Universal) jQuery(function () { SphinxRtdTheme.Navigation.enable(true); });",
    "document_type": "read_the_docs"
  },
  {
    "link": "https://civic.readthedocs.io/en/latest/model/sources/source_types.html",
    "title": "source_types",
    "contents": "Source Types — CIViC documentation About CIViC CIViC Knowledge Model Evidence Items Assertions Features Molecular Profiles Variants Genes Fusions Factors Variant Groups Sources Source Types PubMed Sources ASCO Sources ASH Sources Curating CIViC User Interface and Data CIViC API Get Help CIViC Docs » CIViC Knowledge Model » Sources » Source Types View page source Source Types¶ Each Evidence Item must be associated with a Source Type and Source ID. These data link the Evidence Item to the original publication supporting clinical claims. PubMed Sources¶ For publications indexed on PubMed, the Source ID will be the PubMed ID. The PubMed ID can be found by searching the publication on https://www.ncbi.nlm.nih.gov/pubmed/. ASCO Sources¶ For American Society of Clinical Oncology (ASCO) Sources, the Source ID will be the ASCO Web ID. Of note, the ASCO Web ID is not the ASCO abstract number. The ASCO Web ID is the identification number found in the URL of the abstract. ASH Sources¶ For American Society of Hematology (ASH) Sources, the Source ID will be the DOID for the corresponding abstract publication in the journal Blood. The ASH Abstract DOID can be found on the Blood Journal website entry for the abstract (below the article title). It will look something like this: “10.1182/blood-2021-150273”. Next Previous Visit the CIViC resource at civicdb.org. Disclaimer: CIViC is intended for purely research purposes. It should not be used for emergencies or medical or professional advice. CIViC by The McDonnell Genome Institute at Washington University School of Medicine is licensed under a Creative Commons Public Domain Dedication (CC0 1.0 Universal) jQuery(function () { SphinxRtdTheme.Navigation.enable(true); });",
    "document_type": "read_the_docs"
  },
  {
    "link": "https://civic.readthedocs.io/en/latest/model/evidence.html",
    "title": "evidence",
    "contents": "Evidence Items — CIViC documentation About CIViC CIViC Knowledge Model Evidence Items Evidence Overview Gene Molecular Profile Statement Evidence Level Type Direction Significance Origin Disease Therapy Associated Phenotype Source Clinical Trial Evidence Rating Assertions Features Molecular Profiles Variants Genes Fusions Factors Variant Groups Sources Curating CIViC User Interface and Data CIViC API Get Help CIViC Docs » CIViC Knowledge Model » Evidence Items View page source Evidence Items¶ At the heart of CIViC is the clinical evidence statement. The clinical evidence statement is a piece of information that has been manually curated from trustable medical literature about a molecular profile (variant) or genomic ‘event’ that has implications for protein function, oncogenicity, cancer predisposition, diagnosis (aka molecular classification), prognosis, or predictive response to therapy. For example, “Patients with BRAF V600 mutations respond well to the drug dabrafenib”. A molecular profile is comprised of one or more variant(s) which may be a single nucleotide substitution, a small insertion or deletion, an RNA gene fusion, a chromosomal rearrangement, an RNA expression pattern (e.g. over-expression), etc. Each clinical evidence statement corresponds to a single citable publication. Evidence Items follow a structured knowledge model with required fields: Molecular Profile Name (Gene/Variant), Source, Variant Origin, Disease, Evidence Statement, Evidence Type, Evidence Level, Evidence Direction, Significance, and Trust Rating) with additional optional fields (Associated Phenotypes, etc). For some Evidence Types, additional required or optional fields become available (e.g., Predictive Evidence Types require a Therapy/Drug Name). Evidence Overview Gene Curating Genes Molecular Profile Statement Understanding Evidence Statements Curating Evidence Statements Evidence Level Understanding Evidence Levels Curating Levels Type Understanding Evidence Types Direction Understanding Evidence Direction Curating Evidence Direction Significance Understanding Significance Origin Understanding Variant Origin Curating Variant Origin Disease Curating Diseases Therapy Curating Therapies Associated Phenotype Curating Associated Phenotypes Source Understanding Source Curating Source Clinical Trial Evidence Rating Understanding Evidence Ratings Curating Evidence Ratings Next Previous Visit the CIViC resource at civicdb.org. Disclaimer: CIViC is intended for purely research purposes. It should not be used for emergencies or medical or professional advice. CIViC by The McDonnell Genome Institute at Washington University School of Medicine is licensed under a Creative Commons Public Domain Dedication (CC0 1.0 Universal) jQuery(function () { SphinxRtdTheme.Navigation.enable(true); });",
    "document_type": "read_the_docs"
  },
  {
    "link": "https://civic.readthedocs.io/en/latest/model/evidence/overview.html",
    "title": "overview",
    "contents": "Evidence Overview — CIViC documentation About CIViC CIViC Knowledge Model Evidence Items Evidence Overview Gene Molecular Profile Statement Evidence Level Type Direction Significance Origin Disease Therapy Associated Phenotype Source Clinical Trial Evidence Rating Assertions Features Molecular Profiles Variants Genes Fusions Factors Variant Groups Sources Curating CIViC User Interface and Data CIViC API Get Help CIViC Docs » CIViC Knowledge Model » Evidence Items » Evidence Overview View page source Evidence Overview¶ The following figure shows the attributes of a CIViC Evidence Item, and the options or values available for each. Figure 1: Evidence Item Attributes and Associations The rows in the following table describe the minimal components of a CIViC Evidence Item. Several Evidence Statements are synthesized at the Molecular Profile (Variant) level into a Molecular Profile Description. However, each Evidence Statement is directly linked to a single article in PubMed or ASCO/ASH abstract. More specific guidelines about Evidence Item components can be found in the additional sections outlined in the table of contents. Evidence Attributes Attribute Description Example Source Molecular Profile Gene and Genomic event(s)/mutation(s) (e.g., Single nucleotide variant, Insertion/deletion, Gene fusion, Copy number variant, etc.) implicated. May be a simple comprised of a single variant or a more complex combination of variants. ESR1 Y537S CIViC Statement Human readable interpretation. Free-form text summary of this molecular profile’s potential clinical interpretations. This interpretation is the synthesis of all other information about the alteration(s) and its clinical relevance and should be the living product of active discussion. In this study of 178 non-small cell lung cancer patients, the appearance of EGFR T790M mutation led to resistance to gefitinib. CIViC Evidence Level 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. Level B - Clinical Evidence. CIViC Type 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 six types: Predictive, Prognostic, Diagnostic, Predisposing, Oncogenic and Functional. See ‘Evidence Type’ tab for more information. Predictive - The molecular profile (one or more variants) is predictive of sensitivity or resistance to a therapeutic. CIViC Direction An indicator of whether the evidence statement supports or refutes the significance of an event. See ‘Evidence Type’ tab for more information. Supports - the evidence supports the significance. CIViC Significance The impact of the molecular profile (one or more variants) for predictive, prognostic, diagnostic, oncogenic or functional evidence types. See ‘Evidence Type’ tab for more information. Resistant or Non-response - mutation is associated with resistance to therapy. CIViC Origin Presumed cellular origin of the Variant in samples from the literature citation where the effect of this Variant is being evaluated. Somatic CIViC Disease Specific disease or disease subtype that is associated with this event and its clinical implication. Links directly to Disease Ontology. Estrogen-receptor positive breast cancer (DOID: 0060075). CIViC (Disease Ontology) Associated Phenotype Specific phenotypes associated with the evidence statement. Pancreatic cysts (HP:0001737). The Human Phenotype Ontology (HPO) Therapy For predictive evidence, indicates the therapy for which sensitivity or resistance is indicated (With NCIt ID if available). Tamoxifen, Raloxifene (NCIt IDs: C62078, C62078). CIViC (NCIt) Therapy Interaction Type For predictive evidence involving more than one Therapy, specifies the relationship between the therapies (usually drugs) by indicating whether they are Subtitutes for each other or are used in Sequential or Combination treatments. Substitutes - The therapies listed are often considered to be of the same family, or behave similarly in a treatment setting. CIViC Citation 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. Toy et al., 2013, Nat. Genet. (PMID: 24185512) CIViC (PubMed) PubMed ID PubMed ID for publication where the event was described/explored with direct link to PubMed. 24185512 CIViC (PubMed) Clinical Trial Clinical trial associated with the evidence item. NCT01154140 ClinicalTrials.gov Evidence Rating 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 trust ratings for guidance on how to score an evidence item. 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. CIViC Next Previous Visit the CIViC resource at civicdb.org. Disclaimer: CIViC is intended for purely research purposes. It should not be used for emergencies or medical or professional advice. CIViC by The McDonnell Genome Institute at Washington University School of Medicine is licensed under a Creative Commons Public Domain Dedication (CC0 1.0 Universal) jQuery(function () { SphinxRtdTheme.Navigation.enable(true); });",
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CIViC Bot 03:24 AM

Excerpt: “Six Evidence Types are currently supported: Predictive (i.e. Therapeutic), Diagnostic, Prognostic, Predisposing, Oncogenic, and Functional.” [ 1 ]

CIViC supports the following six Evidence Types (with short meanings):

Predictive — evidence that a molecular profile affects therapeutic response (drug/therapy). [ 1 ]
Diagnostic — evidence that a molecular profile informs diagnosis or disease subtype. [ 1 ]
Prognostic — evidence that a molecular profile predicts disease course, progression, or patient survival. [ 1 ]
Predisposing — evidence (typically germline) that a molecular profile confers susceptibility to disease (includes pathogenicity evaluations). [ 1 ]
Oncogenic — evidence that a somatic variant contributes to tumor pathogenesis (e.g., fits Hallmarks of Cancer). [ 1 ]
Functional — evidence that a variant alters biological or protein function (reference-state changes). [ 1 ]

Note: some Evidence Types enable additional fields when curating (for example, Predictive Evidence requires specifying a Therapy/Drug name). Excerpt: “For some Evidence Types, additional required or optional fields become available (e.g., Predictive Evidence Types require a Therapy/Drug Name).” [ 2 ]

Sources