pharmaobservatory 0.1.3 → 0.1.4

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/BiomarkersApi.md

@@ -9,6 +9,10 @@ All URIs are relative to *https://pharmaobservatory.com*
 | [**biomarkers_biomarker_evidence**](BiomarkersApi.md#biomarkers_biomarker_evidence) | **GET** /api/v1/biomarkers/{id}/biomarker_evidence | Biomarker evidence |
 | [**biomarkers_biomarker_literature**](BiomarkersApi.md#biomarkers_biomarker_literature) | **GET** /api/v1/biomarkers/{id}/biomarker_literature | Trial-cited literature mentions |
 | [**biomarkers_biomarker_publishing_companies**](BiomarkersApi.md#biomarkers_biomarker_publishing_companies) | **GET** /api/v1/biomarkers/{id}/biomarker_publishing_companies | Companies publishing on a biomarker |
+| [**biomarkers_biomarker_relations**](BiomarkersApi.md#biomarkers_biomarker_relations) | **GET** /api/v1/biomarkers/{id}/biomarker_relations | Literature-extracted relations |
+| [**biomarkers_biomarker_sample_coverage**](BiomarkersApi.md#biomarkers_biomarker_sample_coverage) | **GET** /api/v1/biomarkers/{id}/biomarker_sample_coverage | Human sample screening coverage (GDC) |
+| [**biomarkers_biomarker_sample_prevalence**](BiomarkersApi.md#biomarkers_biomarker_sample_prevalence) | **GET** /api/v1/biomarkers/{id}/biomarker_sample_prevalence | Human sample screening reference (GDC cohorts) |
+| [**biomarkers_biomarker_validation**](BiomarkersApi.md#biomarkers_biomarker_validation) | **GET** /api/v1/biomarkers/{id}/biomarker_validation | Biomarker validation ladder |
 | [**biomarkers_biomarker_variant_mentions**](BiomarkersApi.md#biomarkers_biomarker_variant_mentions) | **GET** /api/v1/biomarkers/{id}/biomarker_variant_mentions | Protein variant mentions |
 | [**biomarkers_get**](BiomarkersApi.md#biomarkers_get) | **GET** /api/v1/biomarkers/{id} | One biomarker |
 | [**biomarkers_list**](BiomarkersApi.md#biomarkers_list) | **GET** /api/v1/biomarkers | List biomarkers |
@@ -409,6 +413,322 @@ end
 - **Accept**: application/json
 
 
+## biomarkers_biomarker_relations
+
+> <BiomarkerRelationsResponse> biomarkers_biomarker_relations(id, opts)
+
+Literature-extracted relations
+
+### Examples
+
+```ruby
+require 'time'
+require 'pharmaobservatory'
+# setup authorization
+PharmaObservatory.configure do |config|
+  # Configure Bearer authorization (JWT): ApiBearerJwt
+  config.access_token = 'YOUR_BEARER_TOKEN'
+end
+
+api_instance = PharmaObservatory::BiomarkersApi.new
+id = 'ESR1' # String | 
+opts = {
+  cursor: 'cursor_example', # String | The next_cursor of the previous page. Opaque; it is bound to the filters and the warehouse build that issued it.
+  limit: 56, # Integer | Rows per page, up to 500 (default 50).
+  sort: 'sort_example', # String | Comma separated columns, a leading minus for descending: sort=a,-b.
+  group_by: 'group_by_example', # String | A dimension to group by; a date takes :year, :quarter or :month.
+  measure: 'measure_example' # String | count, sum(col), avg(col), min(col), max(col), median(col) or count_distinct(col).
+}
+
+begin
+  # Literature-extracted relations
+  result = api_instance.biomarkers_biomarker_relations(id, opts)
+  p result
+rescue PharmaObservatory::ApiError => e
+  puts "Error when calling BiomarkersApi->biomarkers_biomarker_relations: #{e}"
+end
+```
+
+#### Using the biomarkers_biomarker_relations_with_http_info variant
+
+This returns an Array which contains the response data, status code and headers.
+
+> <Array(<BiomarkerRelationsResponse>, Integer, Hash)> biomarkers_biomarker_relations_with_http_info(id, opts)
+
+```ruby
+begin
+  # Literature-extracted relations
+  data, status_code, headers = api_instance.biomarkers_biomarker_relations_with_http_info(id, opts)
+  p status_code # => 2xx
+  p headers # => { ... }
+  p data # => <BiomarkerRelationsResponse>
+rescue PharmaObservatory::ApiError => e
+  puts "Error when calling BiomarkersApi->biomarkers_biomarker_relations_with_http_info: #{e}"
+end
+```
+
+### Parameters
+
+| Name | Type | Description | Notes |
+| ---- | ---- | ----------- | ----- |
+| **id** | **String** |  |  |
+| **cursor** | **String** | The next_cursor of the previous page. Opaque; it is bound to the filters and the warehouse build that issued it. | [optional] |
+| **limit** | **Integer** | Rows per page, up to 500 (default 50). | [optional] |
+| **sort** | **String** | Comma separated columns, a leading minus for descending: sort&#x3D;a,-b. | [optional] |
+| **group_by** | **String** | A dimension to group by; a date takes :year, :quarter or :month. | [optional] |
+| **measure** | **String** | count, sum(col), avg(col), min(col), max(col), median(col) or count_distinct(col). | [optional] |
+
+### Return type
+
+[**BiomarkerRelationsResponse**](BiomarkerRelationsResponse.md)
+
+### Authorization
+
+[ApiBearerJwt](../README.md#ApiBearerJwt)
+
+### HTTP request headers
+
+- **Content-Type**: Not defined
+- **Accept**: application/json
+
+
+## biomarkers_biomarker_sample_coverage
+
+> <BiomarkerSampleCoverageResponse> biomarkers_biomarker_sample_coverage(id, opts)
+
+Human sample screening coverage (GDC)
+
+### Examples
+
+```ruby
+require 'time'
+require 'pharmaobservatory'
+# setup authorization
+PharmaObservatory.configure do |config|
+  # Configure Bearer authorization (JWT): ApiBearerJwt
+  config.access_token = 'YOUR_BEARER_TOKEN'
+end
+
+api_instance = PharmaObservatory::BiomarkersApi.new
+id = 'ESR1' # String | 
+opts = {
+  cursor: 'cursor_example', # String | The next_cursor of the previous page. Opaque; it is bound to the filters and the warehouse build that issued it.
+  limit: 56, # Integer | Rows per page, up to 500 (default 50).
+  sort: 'sort_example', # String | Comma separated columns, a leading minus for descending: sort=a,-b.
+  group_by: 'group_by_example', # String | A dimension to group by; a date takes :year, :quarter or :month.
+  measure: 'measure_example' # String | count, sum(col), avg(col), min(col), max(col), median(col) or count_distinct(col).
+}
+
+begin
+  # Human sample screening coverage (GDC)
+  result = api_instance.biomarkers_biomarker_sample_coverage(id, opts)
+  p result
+rescue PharmaObservatory::ApiError => e
+  puts "Error when calling BiomarkersApi->biomarkers_biomarker_sample_coverage: #{e}"
+end
+```
+
+#### Using the biomarkers_biomarker_sample_coverage_with_http_info variant
+
+This returns an Array which contains the response data, status code and headers.
+
+> <Array(<BiomarkerSampleCoverageResponse>, Integer, Hash)> biomarkers_biomarker_sample_coverage_with_http_info(id, opts)
+
+```ruby
+begin
+  # Human sample screening coverage (GDC)
+  data, status_code, headers = api_instance.biomarkers_biomarker_sample_coverage_with_http_info(id, opts)
+  p status_code # => 2xx
+  p headers # => { ... }
+  p data # => <BiomarkerSampleCoverageResponse>
+rescue PharmaObservatory::ApiError => e
+  puts "Error when calling BiomarkersApi->biomarkers_biomarker_sample_coverage_with_http_info: #{e}"
+end
+```
+
+### Parameters
+
+| Name | Type | Description | Notes |
+| ---- | ---- | ----------- | ----- |
+| **id** | **String** |  |  |
+| **cursor** | **String** | The next_cursor of the previous page. Opaque; it is bound to the filters and the warehouse build that issued it. | [optional] |
+| **limit** | **Integer** | Rows per page, up to 500 (default 50). | [optional] |
+| **sort** | **String** | Comma separated columns, a leading minus for descending: sort&#x3D;a,-b. | [optional] |
+| **group_by** | **String** | A dimension to group by; a date takes :year, :quarter or :month. | [optional] |
+| **measure** | **String** | count, sum(col), avg(col), min(col), max(col), median(col) or count_distinct(col). | [optional] |
+
+### Return type
+
+[**BiomarkerSampleCoverageResponse**](BiomarkerSampleCoverageResponse.md)
+
+### Authorization
+
+[ApiBearerJwt](../README.md#ApiBearerJwt)
+
+### HTTP request headers
+
+- **Content-Type**: Not defined
+- **Accept**: application/json
+
+
+## biomarkers_biomarker_sample_prevalence
+
+> <BiomarkerSamplePrevalenceResponse> biomarkers_biomarker_sample_prevalence(id, opts)
+
+Human sample screening reference (GDC cohorts)
+
+### Examples
+
+```ruby
+require 'time'
+require 'pharmaobservatory'
+# setup authorization
+PharmaObservatory.configure do |config|
+  # Configure Bearer authorization (JWT): ApiBearerJwt
+  config.access_token = 'YOUR_BEARER_TOKEN'
+end
+
+api_instance = PharmaObservatory::BiomarkersApi.new
+id = 'ESR1' # String | 
+opts = {
+  cursor: 'cursor_example', # String | The next_cursor of the previous page. Opaque; it is bound to the filters and the warehouse build that issued it.
+  limit: 56, # Integer | Rows per page, up to 500 (default 50).
+  sort: 'sort_example', # String | Comma separated columns, a leading minus for descending: sort=a,-b.
+  group_by: 'group_by_example', # String | A dimension to group by; a date takes :year, :quarter or :month.
+  measure: 'measure_example' # String | count, sum(col), avg(col), min(col), max(col), median(col) or count_distinct(col).
+}
+
+begin
+  # Human sample screening reference (GDC cohorts)
+  result = api_instance.biomarkers_biomarker_sample_prevalence(id, opts)
+  p result
+rescue PharmaObservatory::ApiError => e
+  puts "Error when calling BiomarkersApi->biomarkers_biomarker_sample_prevalence: #{e}"
+end
+```
+
+#### Using the biomarkers_biomarker_sample_prevalence_with_http_info variant
+
+This returns an Array which contains the response data, status code and headers.
+
+> <Array(<BiomarkerSamplePrevalenceResponse>, Integer, Hash)> biomarkers_biomarker_sample_prevalence_with_http_info(id, opts)
+
+```ruby
+begin
+  # Human sample screening reference (GDC cohorts)
+  data, status_code, headers = api_instance.biomarkers_biomarker_sample_prevalence_with_http_info(id, opts)
+  p status_code # => 2xx
+  p headers # => { ... }
+  p data # => <BiomarkerSamplePrevalenceResponse>
+rescue PharmaObservatory::ApiError => e
+  puts "Error when calling BiomarkersApi->biomarkers_biomarker_sample_prevalence_with_http_info: #{e}"
+end
+```
+
+### Parameters
+
+| Name | Type | Description | Notes |
+| ---- | ---- | ----------- | ----- |
+| **id** | **String** |  |  |
+| **cursor** | **String** | The next_cursor of the previous page. Opaque; it is bound to the filters and the warehouse build that issued it. | [optional] |
+| **limit** | **Integer** | Rows per page, up to 500 (default 50). | [optional] |
+| **sort** | **String** | Comma separated columns, a leading minus for descending: sort&#x3D;a,-b. | [optional] |
+| **group_by** | **String** | A dimension to group by; a date takes :year, :quarter or :month. | [optional] |
+| **measure** | **String** | count, sum(col), avg(col), min(col), max(col), median(col) or count_distinct(col). | [optional] |
+
+### Return type
+
+[**BiomarkerSamplePrevalenceResponse**](BiomarkerSamplePrevalenceResponse.md)
+
+### Authorization
+
+[ApiBearerJwt](../README.md#ApiBearerJwt)
+
+### HTTP request headers
+
+- **Content-Type**: Not defined
+- **Accept**: application/json
+
+
+## biomarkers_biomarker_validation
+
+> <BiomarkerValidationResponse> biomarkers_biomarker_validation(id, opts)
+
+Biomarker validation ladder
+
+### Examples
+
+```ruby
+require 'time'
+require 'pharmaobservatory'
+# setup authorization
+PharmaObservatory.configure do |config|
+  # Configure Bearer authorization (JWT): ApiBearerJwt
+  config.access_token = 'YOUR_BEARER_TOKEN'
+end
+
+api_instance = PharmaObservatory::BiomarkersApi.new
+id = 'ESR1' # String | 
+opts = {
+  cursor: 'cursor_example', # String | The next_cursor of the previous page. Opaque; it is bound to the filters and the warehouse build that issued it.
+  limit: 56, # Integer | Rows per page, up to 500 (default 50).
+  sort: 'sort_example', # String | Comma separated columns, a leading minus for descending: sort=a,-b.
+  group_by: 'group_by_example', # String | A dimension to group by; a date takes :year, :quarter or :month.
+  measure: 'measure_example' # String | count, sum(col), avg(col), min(col), max(col), median(col) or count_distinct(col).
+}
+
+begin
+  # Biomarker validation ladder
+  result = api_instance.biomarkers_biomarker_validation(id, opts)
+  p result
+rescue PharmaObservatory::ApiError => e
+  puts "Error when calling BiomarkersApi->biomarkers_biomarker_validation: #{e}"
+end
+```
+
+#### Using the biomarkers_biomarker_validation_with_http_info variant
+
+This returns an Array which contains the response data, status code and headers.
+
+> <Array(<BiomarkerValidationResponse>, Integer, Hash)> biomarkers_biomarker_validation_with_http_info(id, opts)
+
+```ruby
+begin
+  # Biomarker validation ladder
+  data, status_code, headers = api_instance.biomarkers_biomarker_validation_with_http_info(id, opts)
+  p status_code # => 2xx
+  p headers # => { ... }
+  p data # => <BiomarkerValidationResponse>
+rescue PharmaObservatory::ApiError => e
+  puts "Error when calling BiomarkersApi->biomarkers_biomarker_validation_with_http_info: #{e}"
+end
+```
+
+### Parameters
+
+| Name | Type | Description | Notes |
+| ---- | ---- | ----------- | ----- |
+| **id** | **String** |  |  |
+| **cursor** | **String** | The next_cursor of the previous page. Opaque; it is bound to the filters and the warehouse build that issued it. | [optional] |
+| **limit** | **Integer** | Rows per page, up to 500 (default 50). | [optional] |
+| **sort** | **String** | Comma separated columns, a leading minus for descending: sort&#x3D;a,-b. | [optional] |
+| **group_by** | **String** | A dimension to group by; a date takes :year, :quarter or :month. | [optional] |
+| **measure** | **String** | count, sum(col), avg(col), min(col), max(col), median(col) or count_distinct(col). | [optional] |
+
+### Return type
+
+[**BiomarkerValidationResponse**](BiomarkerValidationResponse.md)
+
+### Authorization
+
+[ApiBearerJwt](../README.md#ApiBearerJwt)
+
+### HTTP request headers
+
+- **Content-Type**: Not defined
+- **Accept**: application/json
+
+
 ## biomarkers_biomarker_variant_mentions
 
 > <BiomarkerVariantMentionsResponse> biomarkers_biomarker_variant_mentions(id, opts)

data/docs/BiomarkersRow.md

@@ -13,11 +13,11 @@
 | **gene_symbol** | **String** | The gene symbol. | [optional] |
 | **amino_acid_change** | **String** | The amino-acid change, for a variant. | [optional] |
 | **target_id** | **String** | The target's Ensembl gene id. | [optional] |
-| **hgnc_id** | **String** | The HGNC gene id. | [optional] |
+| **hgnc_id** | **String** | The HUGO Gene Nomenclature Committee (HGNC) gene id. | [optional] |
 | **uniprot_accession** | **String** | The UniProt accession. | [optional] |
 | **feature_code** | **String** | Feature code for a non-gene feature. | [optional] |
 | **feature_type** | **String** | Feature type for a non-gene feature. | [optional] |
-| **evidence_tier** | **Integer** | Strongest evidence tier: 1 FDA companion diagnostic through 6 no evidence. | [optional] |
+| **evidence_tier** | **Integer** | Strongest evidence tier: 1 companion diagnostic of the US Food and Drug Administration (FDA) through 6 no evidence. | [optional] |
 | **evidence_tier_label** | **String** | The tier's name. | [optional] |
 | **n_fda_cdx_assertions** | **Integer** | FDA companion diagnostic assertions. | [optional] |
 | **n_fda_bqp_assertions** | **Integer** | FDA biomarker qualification project assertions. | [optional] |

data/docs/CellLinesRow.md

@@ -21,7 +21,7 @@
 | **cellosaurus_url** | **String** | Link to the Cellosaurus entry. | [optional] |
 | **problem_category** | **String** | The problem category, for a problematic line. | [optional] |
 | **problematic_comment** | **String** | The Cellosaurus comment, for a problematic line. | [optional] |
-| **iclac_registration_ids** | **Array<String>** | ICLAC registration ids. | [optional] |
+| **iclac_registration_ids** | **Array<String>** | International Cell Line Authentication Committee (ICLAC) registration ids. | [optional] |
 | **release_version** | **String** | The Cellosaurus release the check ran against. | [optional] |
 
 ## Example