A JSON representation of the information displayed in VFB term information reports.
The confirms to a standard JSON schema: raw schema docs; schema in browsable form.
Summary reports provide a high-level, tabular summary of VFB term information, provided as a list of dictionaries in JSON, which can be easily loaded into Python Pandas:
import pandas
df = pd.DataFrame.from_records(vc.<some method call>) # Add example...
| Applies to | Column name | content |
|---|---|---|
| all | label | name of entity |
| all | symbol | short symbol for entity (if any) |
| all | id | VFB ID of entity |
| all | tags | tags associated with entity (gross class; data flags) |
| anatomical types & individuals | parents_label | parent class labels (` |
| anatomical types & individuals | parents_id | parent classes IDs (` |
| anatomical individuals | data_source | ID of data_source |
| anatomical individuals | accession | ID of individual in data_source |
| anatomical individuals | dataset | dataset(s) individual belongs to (` |
| anatomical individuals | templates | template(s) registered to (` |
| anatomical individuals | license | license data is available under |
| dataset | description | DataSet description, if present |
| dataset | miniref | minimal information for DataSet reference |
| dataset | FlyBase | FlyBase ID for DataSet reference |
| dataset | PMID | PMID for DataSet reference |
| dataset | DOI | DOI for DataSet reference |
Image download methods save an image manifest to disk, consisting of a tsv with summary info for anatomical individuals depicted in the the downloaded images, with an addition column containing filenames.
Mappings between VFB IDs and external IDs are provided as dictionaries with the form:
{ VFB_id : [{ db: <db> : acc : <acc> }]}
# OR
{ acc : [{ db: <db> : vfb_id : <VFB_id> }]}This structure is necessary because the relationship of VFB_id and external identifier my not always be 1:1. ID mapping methods come with an option to switch between the two representations.
type: type
| column | content |
|---|---|
| upstream_neuron_id | VFB id (short_form) of upstream neuron |
| upstream_neuron_name | name of upstream neuron in VFB |
| weight | weight |
| downstream_neuron_id | VFB id (short_form) of downstream neuron |
| downstream_neuron_name | name of downstream neuron in VFB |
| upstream_class | upstream neuron type(s) (name; ` |
| downstream_class | downstream neuron type(s) (name; ` |
| up_data_source | | | up_accession | | | down_source | | | down_accession | |
Individual: type
| column | content |
|---|---|
| query_neuron_id | VFB id (short_form) of query neuron |
| query_neuron_name | name of query neuron in VFB |
| weight | weight |
| target_neuron_id | VFB id (short_form) of target neuron |
| target_neuron_name | name of target neuron in VFB |
Similarity
| column | content | | id | VFB id (short_form) of target neuron | | NBLAST_score | | | label | | | types | | | source_id | | | accession_in_source | |