nickdos
commented
2 years ago Dumping the full list of fields sorted by most populated, extracted from notebook:
| field | count of rows with values |
|---|---|
| organization.approval_status | 48438 |
| revision_id | 48438 |
| organization.type | 48438 |
| organization.revision_id | 48438 |
| organization.image_url | 48438 |
| organization.state | 48438 |
| organization.is_organization | 48438 |
| organization.name | 48438 |
| num_resources | 48438 |
| organization.title | 48438 |
| groups | 48438 |
| organization.created | 48438 |
| relationships_as_subject | 48438 |
| tags | 48438 |
| organization.description | 48438 |
| metadata_modified | 48438 |
| creator_user_id | 48438 |
| id | 48438 |
| private | 48438 |
| metadata_created | 48438 |
| num_tags | 48438 |
| relationships_as_object | 48438 |
| type | 48438 |
| organization.id | 48438 |
| state | 48438 |
| isopen | 48438 |
| owner_org | 48438 |
| resources | 48438 |
| title | 48438 |
| name | 48438 |
| notes | 48438 |
| resource_permissions | 48410 |
| sequence_data_type | 48406 |
| ticket | 48367 |
| license_id | 48329 |
| license_title | 48329 |
| date_of_transfer | 46165 |
| data_type | 46162 |
| access_control_date | 45927 |
| access_control_mode | 45927 |
| access_control_reason | 45927 |
| sample_id | 45118 |
| folder_name | 44402 |
| description | 44402 |
| spatial | 41229 |
| analysis_software_version | 38107 |
| flow_id | 36852 |
| amplicon | 36480 |
| reads | 36166 |
| target | 36060 |
| comments | 36000 |
| data_generated | 34460 |
| latitude | 34223 |
| longitude | 34215 |
| sample_submission_date | 33628 |
| facility | 33093 |
| base_url | 33010 |
| sample_type | 31622 |
| collection_date | 31029 |
| vegetation_type | 30232 |
| texture | 30206 |
| color | 30143 |
| url | 30139 |
| coastal_id | 30090 |
| citation | 30084 |
| nrs_trip_code | 30061 |
| nrs_sample_code | 30061 |
| host_state | 30056 |
| touching_organisms | 30053 |
| fouling_organisms | 30053 |
| information | 30053 |
| grazing_number | 30053 |
| fire_intensity_if_known | 30052 |
| crop_rotation_4yrs_since_present | 30052 |
| voyage_code | 30052 |
| crop_rotation_3yrs_since_present | 30052 |
| funding_agency | 30052 |
| utc_time_sampled | 30052 |
| imos_site_code | 30052 |
| voyage_survey_link | 30052 |
| sample_attribution | 30052 |
| crop_rotation_5yrs_since_present | 30052 |
| date_since_change_in_land_use | 30052 |
| flooding | 30052 |
| crop_rotation_2yrs_since_present | 30052 |
| fire | 30052 |
| sample_submitter | 30052 |
top 86 results
API documentation: https://docs.ckan.org/en/latest/api/ Full package list from API: https://data.bioplatforms.com/api/3/action/package_list Tag list: https://data.bioplatforms.com/api/3/action/tag_list Schema doc: https://docs.google.com/spreadsheets/d/1wgNknGPWhlyLU6BBpB2eV2T0eoyTrFf_/edit#gid=1783503621
To get individual records from either the
package_listusing the output as anID. E.g. https://data.bioplatforms.com/api/3/action/package_show?id=bpa-tsi-pacbio-hifi-357366-da052899https://usersupport.bioplatforms.com/programmatic_access.html
https://data.bioplatforms.com/api/3/action/package_search?q=:&rows=1000 seems to work - need to paginate at 1000 records (hard limit) -
48,438records found, asme number reported on https://data.bioplatforms.com/dataset. Help doc linked.Just creating a placeholder for noting down snippets of info.
Downloading a single dataset results in a ZIP file with the following structure - e.g. from https://data.bioplatforms.com/dataset/bpa-tsi-illumina-shortread-357596-h3vnhdsx2
The
package_metadatadirectory contains a CSV file with the following column headings:Organization | Title | Description | URL | Tags | Geospatial Coverage | License | Resource Permissions | Access Control Reason | Access Control Date | Access Control Mode | Sequence Data Type | Related Data | analysis_software | analysis_software_version | base_url | ccg_jira_ticket | cell_postion | data_context | data_custodian | data_generated | data_type | dataset_id | date_of_transfer | date_of_transfer_to_archive | decimal_latitude_public | decimal_longitude_public | description | dna_treatment | download | experimental_design | facility_project_code | facility_sample_id | file_count | file_name | file_type | flow_cell_id | flowcell_id | flowcell_type | folder_name | genus | insert_size_range | latitude | library_comments | library_construction_protocol | library_id | library_index_id | library_index_sequence | library_layout | library_location | library_ng_ul | library_oligo_sequence | library_pcr_cycles | library_pcr_reps | library_prep_date | library_prepared_by | library_selection | library_source | library_status | library_strategy | library_type | longitude | movie_length | n_libraries_pooled | name | notes | run_format | sample_id | sequencing_facility | sequencing_kit_chemistry_version | sequencing_model | sequencing_platform | species | specimen_id | ticket | tissue_number | work_orderThe
organization_metdatadirectory contains a CSV file with this data:The
resource_metadatadirectory contains a CSV with data: