pharmaobservatory 0.1.2 → 0.1.4

data/docs/BiomarkerRelationsRow.md

@@ -0,0 +1,54 @@
+# PharmaObservatory::BiomarkerRelationsRow
+
+## Properties
+
+| Name | Type | Description | Notes |
+| ---- | ---- | ----------- | ----- |
+| **route_key** | **String** | The biomarker's own route key, the entry key for the biomarkers object type (the gene symbol for a gene, the variant key for a protein variant). | [optional] |
+| **biomarker_id** | **String** | The biomarker's key. | [optional] |
+| **biomarker_kind** | **String** | Whether the row describes a gene or a protein variant. | [optional] |
+| **gene_symbol** | **String** | The gene symbol. | [optional] |
+| **amino_acid_change** | **String** | The protein change, for a variant. | [optional] |
+| **related_entity_kind** | **String** | The kind of the related entity (gene, drug or condition). | [optional] |
+| **related_entity_id** | **String** | The related entity's key in its own vocabulary (a gene symbol, a drug id such as unii:..., or a condition key). | [optional] |
+| **related_display_name** | **String** | The related entity's name. | [optional] |
+| **relation_type** | **String** | The source's relation label, as the source states it. | [optional] |
+| **pmid** | **String** | The PubMed id of the paper the relation was extracted from. | [optional] |
+| **title** | **String** | The paper's title. | [optional] |
+| **journal_nlm_id** | **String** | The journal's National Library of Medicine (NLM) id. | [optional] |
+| **journal_title** | **String** | The journal's title. | [optional] |
+| **pub_year** | **Integer** | The paper's publication year. | [optional] |
+| **n_source_assertions** | **Integer** | Source assertions of this relation in the paper. | [optional] |
+| **n_relation_papers** | **Integer** | Papers that carry this biomarker, related entity and relation label. | [optional] |
+| **evidence_type** | **String** | The evidence type (a text-mined relation, never a clinical claim). | [optional] |
+| **source** | **String** | The source of the evidence. | [optional] |
+| **display_order** | **Integer** | The order the web page lists the relation in within its kind. | [optional] |
+
+## Example
+
+```ruby
+require 'pharmaobservatory'
+
+instance = PharmaObservatory::BiomarkerRelationsRow.new(
+  route_key: null,
+  biomarker_id: null,
+  biomarker_kind: null,
+  gene_symbol: null,
+  amino_acid_change: null,
+  related_entity_kind: null,
+  related_entity_id: null,
+  related_display_name: null,
+  relation_type: null,
+  pmid: null,
+  title: null,
+  journal_nlm_id: null,
+  journal_title: null,
+  pub_year: null,
+  n_source_assertions: null,
+  n_relation_papers: null,
+  evidence_type: null,
+  source: null,
+  display_order: null
+)
+```
+

data/docs/BiomarkerSampleCoverageResponse.md

@@ -0,0 +1,58 @@
+# PharmaObservatory::BiomarkerSampleCoverageResponse
+
+## Properties
+
+| Name | Type | Description | Notes |
+| ---- | ---- | ----------- | ----- |
+| **dataset** | **String** |  |  |
+| **grain** | **String** |  | [optional] |
+| **object_type** | **String** |  | [optional] |
+| **id** | **String** |  | [optional] |
+| **scope** | [**BiomarkerCdxAssertionsResponseScope**](BiomarkerCdxAssertionsResponseScope.md) |  | [optional] |
+| **columns** | [**Array<DatasetColumn>**](DatasetColumn.md) |  |  |
+| **rows** | [**Array<BiomarkerSampleCoverageRow>**](BiomarkerSampleCoverageRow.md) |  |  |
+| **total** | **Integer** | The exact count of the filtered rows on an ungrouped read, carried by the cursor; null when grouped. | [optional] |
+| **next_cursor** | **String** |  | [optional] |
+| **sort** | **Array<String>** |  | [optional] |
+| **filters** | **Array<Hash<String, Object>>** |  | [optional] |
+| **group_by** | **Array<String>** |  | [optional] |
+| **measures** | **Array<String>** |  | [optional] |
+| **attribution** | [**Array<DatasetAttribution>**](DatasetAttribution.md) |  | [optional] |
+| **source_credit** | **String** |  | [optional] |
+| **withheld_tiers** | **Array<String>** |  | [optional] |
+| **withheld_columns** | **Array<String>** |  | [optional] |
+| **freshness** | [**BiomarkerCdxAssertionsResponseFreshness**](BiomarkerCdxAssertionsResponseFreshness.md) |  | [optional] |
+| **build** | [**BiomarkerCdxAssertionsResponseBuild**](BiomarkerCdxAssertionsResponseBuild.md) |  | [optional] |
+| **build_state** | [**DatasetBuildState**](DatasetBuildState.md) |  | [optional] |
+| **restriction** | **Hash<String, Object>** |  | [optional] |
+
+## Example
+
+```ruby
+require 'pharmaobservatory'
+
+instance = PharmaObservatory::BiomarkerSampleCoverageResponse.new(
+  dataset: null,
+  grain: null,
+  object_type: null,
+  id: null,
+  scope: null,
+  columns: null,
+  rows: null,
+  total: null,
+  next_cursor: null,
+  sort: null,
+  filters: null,
+  group_by: null,
+  measures: null,
+  attribution: null,
+  source_credit: null,
+  withheld_tiers: null,
+  withheld_columns: null,
+  freshness: null,
+  build: null,
+  build_state: null,
+  restriction: null
+)
+```
+

data/docs/BiomarkerSampleCoverageRow.md

@@ -0,0 +1,36 @@
+# PharmaObservatory::BiomarkerSampleCoverageRow
+
+## Properties
+
+| Name | Type | Description | Notes |
+| ---- | ---- | ----------- | ----- |
+| **route_key** | **String** | The route key of the gene the variants belong to, the entry key for the biomarkers object type. | [optional] |
+| **gene_symbol** | **String** | The gene symbol. | [optional] |
+| **variant_biomarker_id** | **String** | The variant's own biomarker key. | [optional] |
+| **variant_route_key** | **String** | The variant's own route key (the id its web page uses). | [optional] |
+| **amino_acid_change** | **String** | The protein change, for example p.V600E. | [optional] |
+| **gdc_data_release** | **String** | The Genomic Data Commons data release the match was made against. | [optional] |
+| **normalization_status** | **String** | How the variant matched: resolved_single_ssm, no_exact_ssm, multiple_exact_ssms or source_error. | [optional] |
+| **match_count** | **Integer** | Somatic mutations in the catalogue that encode the same protein change. | [optional] |
+| **resolution_reason** | **String** | The reason for the status, in words. | [optional] |
+| **measured_project_count** | **Integer** | Research projects with an observed frequency for the variant in biomarker_sample_prevalence. | [optional] |
+
+## Example
+
+```ruby
+require 'pharmaobservatory'
+
+instance = PharmaObservatory::BiomarkerSampleCoverageRow.new(
+  route_key: null,
+  gene_symbol: null,
+  variant_biomarker_id: null,
+  variant_route_key: null,
+  amino_acid_change: null,
+  gdc_data_release: null,
+  normalization_status: null,
+  match_count: null,
+  resolution_reason: null,
+  measured_project_count: null
+)
+```
+

data/docs/BiomarkerSamplePrevalenceResponse.md

@@ -0,0 +1,58 @@
+# PharmaObservatory::BiomarkerSamplePrevalenceResponse
+
+## Properties
+
+| Name | Type | Description | Notes |
+| ---- | ---- | ----------- | ----- |
+| **dataset** | **String** |  |  |
+| **grain** | **String** |  | [optional] |
+| **object_type** | **String** |  | [optional] |
+| **id** | **String** |  | [optional] |
+| **scope** | [**BiomarkerCdxAssertionsResponseScope**](BiomarkerCdxAssertionsResponseScope.md) |  | [optional] |
+| **columns** | [**Array<DatasetColumn>**](DatasetColumn.md) |  |  |
+| **rows** | [**Array<BiomarkerSamplePrevalenceRow>**](BiomarkerSamplePrevalenceRow.md) |  |  |
+| **total** | **Integer** | The exact count of the filtered rows on an ungrouped read, carried by the cursor; null when grouped. | [optional] |
+| **next_cursor** | **String** |  | [optional] |
+| **sort** | **Array<String>** |  | [optional] |
+| **filters** | **Array<Hash<String, Object>>** |  | [optional] |
+| **group_by** | **Array<String>** |  | [optional] |
+| **measures** | **Array<String>** |  | [optional] |
+| **attribution** | [**Array<DatasetAttribution>**](DatasetAttribution.md) |  | [optional] |
+| **source_credit** | **String** |  | [optional] |
+| **withheld_tiers** | **Array<String>** |  | [optional] |
+| **withheld_columns** | **Array<String>** |  | [optional] |
+| **freshness** | [**BiomarkerCdxAssertionsResponseFreshness**](BiomarkerCdxAssertionsResponseFreshness.md) |  | [optional] |
+| **build** | [**BiomarkerCdxAssertionsResponseBuild**](BiomarkerCdxAssertionsResponseBuild.md) |  | [optional] |
+| **build_state** | [**DatasetBuildState**](DatasetBuildState.md) |  | [optional] |
+| **restriction** | **Hash<String, Object>** |  | [optional] |
+
+## Example
+
+```ruby
+require 'pharmaobservatory'
+
+instance = PharmaObservatory::BiomarkerSamplePrevalenceResponse.new(
+  dataset: null,
+  grain: null,
+  object_type: null,
+  id: null,
+  scope: null,
+  columns: null,
+  rows: null,
+  total: null,
+  next_cursor: null,
+  sort: null,
+  filters: null,
+  group_by: null,
+  measures: null,
+  attribution: null,
+  source_credit: null,
+  withheld_tiers: null,
+  withheld_columns: null,
+  freshness: null,
+  build: null,
+  build_state: null,
+  restriction: null
+)
+```
+

data/docs/BiomarkerSamplePrevalenceRow.md

@@ -0,0 +1,56 @@
+# PharmaObservatory::BiomarkerSamplePrevalenceRow
+
+## Properties
+
+| Name | Type | Description | Notes |
+| ---- | ---- | ----------- | ----- |
+| **route_key** | **String** | The route key of the gene the variants belong to, the entry key for the biomarkers object type. | [optional] |
+| **gene_symbol** | **String** | The gene symbol. | [optional] |
+| **variant_biomarker_id** | **String** | The variant's own biomarker key. | [optional] |
+| **variant_route_key** | **String** | The variant's own route key (the id its web page uses). | [optional] |
+| **amino_acid_change** | **String** | The protein change, for example p.V600E. | [optional] |
+| **gdc_ssm_id** | **String** | The identifier of the somatic mutation in the Genomic Data Commons. | [optional] |
+| **gdc_project_id** | **String** | The Genomic Data Commons research project (cohort) the counts come from. | [optional] |
+| **gdc_project_name** | **String** | The name of the research project. | [optional] |
+| **condition_id** | **String** | The condition key (a MeSH, Medical Subject Headings, descriptor id) the project's disease maps to, where one is mapped. | [optional] |
+| **condition_name** | **String** | The mapped condition's MeSH heading. | [optional] |
+| **source_disease_types** | **Array<String>** | The disease types the source states for the project. | [optional] |
+| **source_primary_sites** | **Array<String>** | The primary sites the source states for the project. | [optional] |
+| **affected_case_count** | **Integer** | Cases in the cohort with the exact variant. | [optional] |
+| **ssm_profiled_case_count** | **Integer** | Cases in the cohort profiled for somatic mutations, the denominator of the observed frequency. | [optional] |
+| **all_case_count** | **Integer** | All cases in the project. | [optional] |
+| **observed_frequency** | **Float** | Affected cases over mutation-profiled cases in this cohort. | [optional] |
+| **frequency_ci95_low** | **Float** | Lower bound of the 95 percent confidence interval of the observed frequency. | [optional] |
+| **frequency_ci95_high** | **Float** | Upper bound of the 95 percent confidence interval of the observed frequency. | [optional] |
+| **gdc_data_release** | **String** | The Genomic Data Commons data release the counts come from. | [optional] |
+| **claim_type** | **String** | What the figure states; an observed frequency in a named cohort. | [optional] |
+
+## Example
+
+```ruby
+require 'pharmaobservatory'
+
+instance = PharmaObservatory::BiomarkerSamplePrevalenceRow.new(
+  route_key: null,
+  gene_symbol: null,
+  variant_biomarker_id: null,
+  variant_route_key: null,
+  amino_acid_change: null,
+  gdc_ssm_id: null,
+  gdc_project_id: null,
+  gdc_project_name: null,
+  condition_id: null,
+  condition_name: null,
+  source_disease_types: null,
+  source_primary_sites: null,
+  affected_case_count: null,
+  ssm_profiled_case_count: null,
+  all_case_count: null,
+  observed_frequency: null,
+  frequency_ci95_low: null,
+  frequency_ci95_high: null,
+  gdc_data_release: null,
+  claim_type: null
+)
+```
+

data/docs/BiomarkerValidationResponse.md

@@ -0,0 +1,58 @@
+# PharmaObservatory::BiomarkerValidationResponse
+
+## Properties
+
+| Name | Type | Description | Notes |
+| ---- | ---- | ----------- | ----- |
+| **dataset** | **String** |  |  |
+| **grain** | **String** |  | [optional] |
+| **object_type** | **String** |  | [optional] |
+| **id** | **String** |  | [optional] |
+| **scope** | [**BiomarkerCdxAssertionsResponseScope**](BiomarkerCdxAssertionsResponseScope.md) |  | [optional] |
+| **columns** | [**Array<DatasetColumn>**](DatasetColumn.md) |  |  |
+| **rows** | [**Array<BiomarkerValidationRow>**](BiomarkerValidationRow.md) |  |  |
+| **total** | **Integer** | The exact count of the filtered rows on an ungrouped read, carried by the cursor; null when grouped. | [optional] |
+| **next_cursor** | **String** |  | [optional] |
+| **sort** | **Array<String>** |  | [optional] |
+| **filters** | **Array<Hash<String, Object>>** |  | [optional] |
+| **group_by** | **Array<String>** |  | [optional] |
+| **measures** | **Array<String>** |  | [optional] |
+| **attribution** | [**Array<DatasetAttribution>**](DatasetAttribution.md) |  | [optional] |
+| **source_credit** | **String** |  | [optional] |
+| **withheld_tiers** | **Array<String>** |  | [optional] |
+| **withheld_columns** | **Array<String>** |  | [optional] |
+| **freshness** | [**BiomarkerCdxAssertionsResponseFreshness**](BiomarkerCdxAssertionsResponseFreshness.md) |  | [optional] |
+| **build** | [**BiomarkerCdxAssertionsResponseBuild**](BiomarkerCdxAssertionsResponseBuild.md) |  | [optional] |
+| **build_state** | [**DatasetBuildState**](DatasetBuildState.md) |  | [optional] |
+| **restriction** | **Hash<String, Object>** |  | [optional] |
+
+## Example
+
+```ruby
+require 'pharmaobservatory'
+
+instance = PharmaObservatory::BiomarkerValidationResponse.new(
+  dataset: null,
+  grain: null,
+  object_type: null,
+  id: null,
+  scope: null,
+  columns: null,
+  rows: null,
+  total: null,
+  next_cursor: null,
+  sort: null,
+  filters: null,
+  group_by: null,
+  measures: null,
+  attribution: null,
+  source_credit: null,
+  withheld_tiers: null,
+  withheld_columns: null,
+  freshness: null,
+  build: null,
+  build_state: null,
+  restriction: null
+)
+```
+

data/docs/BiomarkerValidationRow.md

@@ -0,0 +1,70 @@
+# PharmaObservatory::BiomarkerValidationRow
+
+## Properties
+
+| Name | Type | Description | Notes |
+| ---- | ---- | ----------- | ----- |
+| **biomarker_validation_id** | **String** | The evidence assertion id. | [optional] |
+| **route_key** | **String** | The biomarker's route key, the entry key for the biomarkers object type; for a gene it is the gene symbol. | [optional] |
+| **gene_symbol** | **String** | The gene symbol (HGNC, the HUGO Gene Nomenclature Committee). | [optional] |
+| **biomarker_id** | **String** | The biomarker key. | [optional] |
+| **biomarker_display_name** | **String** | The biomarker's display name. | [optional] |
+| **biomarker_kind** | **String** | The kind of biomarker the evidence is filed against. | [optional] |
+| **organization_name** | **String** | The organization that can supply the evidence, as the source names it (null when the source names none that resolved). | [optional] |
+| **organization_org_id** | **String** | Legal-entity level: the organization record (null when unresolved). | [optional] |
+| **organization_company_id** | **String** | Company level: the organization's company (null when unresolved). | [optional] |
+| **organization_company_name** | **String** | Display name of the organization's company. | [optional] |
+| **organization_group_id** | **String** | Group level: the organization's current ultimate parent; a root's group is itself. | [optional] |
+| **organization_group_name** | **String** | Display name of the organization's group. | [optional] |
+| **organization_role** | **String** | What the organization is to the evidence: lead_sponsor, collaborator, contract_vendor, assay_manufacturer, qualification_submitter, testing_lab or publishing_org. | [optional] |
+| **organization_match_tier** | **String** | How the organization name matched an organization record. | [optional] |
+| **tier** | **Integer** | The rung on the validation ladder, 1 to 4. A rung is a kind of evidence, never a score: rows are not ranked across organizations or evidence types. | [optional] |
+| **tier_label** | **String** | The rung's name, for example fda_authorized_companion_diagnostic or named_in_inclusion_criteria. | [optional] |
+| **evidence_type** | **String** | The evidence lane: fda_bqp_qualification, fda_cdx_authorization, aact_endpoint_role, aact_eligibility_section, aact_biospecimen, trial_mention or clinvar_clinical_testing. | [optional] |
+| **evidence_count** | **Integer** | Sibling rows sharing this biomarker, organization and role. Not the number of source records behind a ClinVar row (clinvar_scv_count). | [optional] |
+| **evidence_ref** | **String** | The source reference the row cites. | [optional] |
+| **evidence_ref_kind** | **String** | What kind of reference evidence_ref is. | [optional] |
+| **trial_id** | **String** | The trial key (an NCT id) when the evidence is a trial; null otherwise. | [optional] |
+| **citation_url** | **String** | A link to the cited record. | [optional] |
+| **citation_verified** | **Boolean** | False for the FDA Biomarker Qualification Program arm, whose captured links are known to go stale; true otherwise. A link marked false may not resolve. | [optional] |
+| **evidence_snippet** | **String** | The text span the evidence rests on, where the source gives one. | [optional] |
+| **biomarker_role** | **String** | The biomarker's role in the evidence, where the source states it. | [optional] |
+| **is_surrogate_endpoint_claim** | **Boolean** | True when the evidence is a claim that the biomarker is a surrogate endpoint. | [optional] |
+| **clinvar_scv_count** | **Integer** | For a ClinVar row, the number of ClinVar submission records the row collapses; null otherwise. | [optional] |
+
+## Example
+
+```ruby
+require 'pharmaobservatory'
+
+instance = PharmaObservatory::BiomarkerValidationRow.new(
+  biomarker_validation_id: null,
+  route_key: null,
+  gene_symbol: null,
+  biomarker_id: null,
+  biomarker_display_name: null,
+  biomarker_kind: null,
+  organization_name: null,
+  organization_org_id: null,
+  organization_company_id: null,
+  organization_company_name: null,
+  organization_group_id: null,
+  organization_group_name: null,
+  organization_role: null,
+  organization_match_tier: null,
+  tier: null,
+  tier_label: null,
+  evidence_type: null,
+  evidence_count: null,
+  evidence_ref: null,
+  evidence_ref_kind: null,
+  trial_id: null,
+  citation_url: null,
+  citation_verified: null,
+  evidence_snippet: null,
+  biomarker_role: null,
+  is_surrogate_endpoint_claim: null,
+  clinvar_scv_count: null
+)
+```
+

data/docs/BiomarkerVariantMentionsResponse.md

@@ -0,0 +1,58 @@
+# PharmaObservatory::BiomarkerVariantMentionsResponse
+
+## Properties
+
+| Name | Type | Description | Notes |
+| ---- | ---- | ----------- | ----- |
+| **dataset** | **String** |  |  |
+| **grain** | **String** |  | [optional] |
+| **object_type** | **String** |  | [optional] |
+| **id** | **String** |  | [optional] |
+| **scope** | [**BiomarkerCdxAssertionsResponseScope**](BiomarkerCdxAssertionsResponseScope.md) |  | [optional] |
+| **columns** | [**Array<DatasetColumn>**](DatasetColumn.md) |  |  |
+| **rows** | [**Array<BiomarkerVariantMentionsRow>**](BiomarkerVariantMentionsRow.md) |  |  |
+| **total** | **Integer** | The exact count of the filtered rows on an ungrouped read, carried by the cursor; null when grouped. | [optional] |
+| **next_cursor** | **String** |  | [optional] |
+| **sort** | **Array<String>** |  | [optional] |
+| **filters** | **Array<Hash<String, Object>>** |  | [optional] |
+| **group_by** | **Array<String>** |  | [optional] |
+| **measures** | **Array<String>** |  | [optional] |
+| **attribution** | [**Array<DatasetAttribution>**](DatasetAttribution.md) |  | [optional] |
+| **source_credit** | **String** |  | [optional] |
+| **withheld_tiers** | **Array<String>** |  | [optional] |
+| **withheld_columns** | **Array<String>** |  | [optional] |
+| **freshness** | [**BiomarkerCdxAssertionsResponseFreshness**](BiomarkerCdxAssertionsResponseFreshness.md) |  | [optional] |
+| **build** | [**BiomarkerCdxAssertionsResponseBuild**](BiomarkerCdxAssertionsResponseBuild.md) |  | [optional] |
+| **build_state** | [**DatasetBuildState**](DatasetBuildState.md) |  | [optional] |
+| **restriction** | **Hash<String, Object>** |  | [optional] |
+
+## Example
+
+```ruby
+require 'pharmaobservatory'
+
+instance = PharmaObservatory::BiomarkerVariantMentionsResponse.new(
+  dataset: null,
+  grain: null,
+  object_type: null,
+  id: null,
+  scope: null,
+  columns: null,
+  rows: null,
+  total: null,
+  next_cursor: null,
+  sort: null,
+  filters: null,
+  group_by: null,
+  measures: null,
+  attribution: null,
+  source_credit: null,
+  withheld_tiers: null,
+  withheld_columns: null,
+  freshness: null,
+  build: null,
+  build_state: null,
+  restriction: null
+)
+```
+

data/docs/BiomarkerVariantMentionsRow.md

@@ -0,0 +1,44 @@
+# PharmaObservatory::BiomarkerVariantMentionsRow
+
+## Properties
+
+| Name | Type | Description | Notes |
+| ---- | ---- | ----------- | ----- |
+| **route_key** | **String** | The route key of the gene the variants belong to, the entry key for the biomarkers object type. | [optional] |
+| **gene_symbol** | **String** | The gene symbol. | [optional] |
+| **variant_biomarker_id** | **String** | The variant's own biomarker key. | [optional] |
+| **variant_route_key** | **String** | The variant's own route key (the id its web page uses). | [optional] |
+| **display_name** | **String** | The variant's display name. | [optional] |
+| **amino_acid_change** | **String** | The protein change, for example V600E. | [optional] |
+| **biomarker_kind** | **String** | The kind of biomarker the row describes (a protein variant). | [optional] |
+| **evidence_type** | **String** | The evidence type (a literature mention, never an actionability claim). | [optional] |
+| **source** | **String** | The source of the evidence. | [optional] |
+| **n_papers** | **Integer** | Distinct papers that name the variant. | [optional] |
+| **first_publication_year** | **Integer** | Earliest publication year. | [optional] |
+| **last_publication_year** | **Integer** | Latest publication year. | [optional] |
+| **sample_pmids** | **Array<String>** | Up to five sample PubMed ids, newest first. | [optional] |
+| **sample_citations** | **Array<String>** | Up to five sample citations, newest first. | [optional] |
+
+## Example
+
+```ruby
+require 'pharmaobservatory'
+
+instance = PharmaObservatory::BiomarkerVariantMentionsRow.new(
+  route_key: null,
+  gene_symbol: null,
+  variant_biomarker_id: null,
+  variant_route_key: null,
+  display_name: null,
+  amino_acid_change: null,
+  biomarker_kind: null,
+  evidence_type: null,
+  source: null,
+  n_papers: null,
+  first_publication_year: null,
+  last_publication_year: null,
+  sample_pmids: null,
+  sample_citations: null
+)
+```
+