VFB_connect output formats
==========================

VFB_JSON
--------

A JSON representation of the information displayed in VFB term
information reports.

The confirms to a standard JSON schema: `raw schema
docs <https://github.com/VirtualFlyBrain/VFB_json_schema/blob/master/src/json_schema/vfb_termInfo.json>`__;
`schema in browsable form <https://virtualflybrain.github.io/VFB_json_schema/doc/schema_doc.html>`__.

Summary reports
---------------

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:

.. code:: Python

   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 &      | parents_label | parent class labels (\` |
| individuals             |               |                         |
+-------------------------+---------------+-------------------------+
| anatomical types &      | parents_id    | parent classes IDs (\`  |
| individuals             |               |                         |
+-------------------------+---------------+-------------------------+
| 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 manifest
~~~~~~~~~~~~~~

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.

ID Mappings
-----------

Mappings between VFB IDs and external IDs are provided as dictionaries
with the form:

.. code:: Python

   { 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.

.. _connectomics--neuron-similarity-reports:

Connectomics & neuron similarity reports
----------------------------------------

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 \| \|