Database 
========

ARC Metadata Registry application leverages the abstract ISA-JSON format to maintain the experimental metadata. Also, the application maintains the metadata related to the ARCs from individual DataHUBs. The backend database contains three important document collections

ARC Metadata Collection
-----------------------

Each document within ARC Metadata collection contains the file-level information of each ARCs. Each file-level change to the ARCs in the DataHUB is maintained as separate ARC version to present the evolution of the individual ARCs by keeping track of the history of the ARC updates.   


.. literalinclude:: _static/isajson/arc_metadata.json
    :language: json

Parameter-Values Collection
---------------------------

This collection maintains each parameter-value from both the ARC and experimental metadata. The collection maintains the characteristics, components, factors, study and assay parameters values from the ISA data of individual ARCs.


.. literalinclude:: _static/isajson/parameter_values.json
    :language: json

Investigation Data Collection  
-----------------------------

.. note::
   In the `ISA Metadata Framework <https://isa-specs.readthedocs.io/en/latest/isajson.html>`_ specification, there are instances which are not assigned to a specific data type, instead, a complex type with "anyOf" marker. In order to maintain these fields in the database collections, they are translated and stored by a field with the same name and type as suffix. 

**investigation_schema.json**

This schema implements Investigation from the ISA Abstract Model.

.. literalinclude:: _static/isajson/investigation_schema.json
    :language: json

**study_schema.json**

This schema implements Study from the ISA Abstract Model.

.. literalinclude:: _static/isajson/study_schema.json
    :language: json

**assay_schema.json**

This schema implements Assay from the ISA Abstract Model.

.. literalinclude:: _static/isajson/assay_schema.json
    :language: json

**comment_schema.json**

This schema implements the ability to annotate objects with user-defined comments.

.. literalinclude:: _static/isajson/comment_schema.json
    :language: json

**data_schema.json**

This schema implements Data from the ISA Abstract Model.

.. literalinclude:: _static/isajson/data_schema.json
    :language: json

**factor_schema.json**

This schema implements Study factor from the ISA Abstract Model.

.. literalinclude:: _static/isajson/factor_schema.json
    :language: json

**factor_value_schema.json**

This schema implements Factor value given to a node corresponding to a declared Factor.

.. literalinclude:: _static/isajson/factor_value_schema.json
    :language: json

**material_attribute_schema.json**

This schema is used in a Material node to declare an attribute (Characteristic).

.. literalinclude:: _static/isajson/material_attribute_schema.json
    :language: json

**material_attribute_value_schema.json**

This schema is used in a Material node to hold an attribute value (value of a Characteristic).

.. literalinclude:: _static/isajson/material_attribute_value_schema.json
    :language: json

**material_schema.json**

This schema implements Material nodes from the ISA Abstract Model.

.. literalinclude:: _static/isajson/material_schema.json
    :language: json

**ontology_annotation_schema.json**

This schema implements Ontology from the ISA Abstract Model.

.. literalinclude:: _static/isajson/ontology_annotation_schema.json
    :language: json

**ontology_source_reference_schema.json**

This schema implements Ontology from the ISA Abstract Model.

.. literalinclude:: _static/isajson/ontology_source_reference_schema.json
    :language: json

**person_schema.json**

This schema implements Contact from the ISA Abstract Model.

.. literalinclude:: _static/isajson/person_schema.json
    :language: json

**process_parameter_value_schema.json**

This schema is used in a Process node to hold a parameter value (value of a Protocol parameter).

.. literalinclude:: _static/isajson/process_parameter_value_schema.json
    :language: json

**process_schema.json**

This schema implements Process nodes from the ISA Abstract Model.

.. literalinclude:: _static/isajson/process_schema.json
    :language: json

**protocol_parameter_schema.json**

This schema is used in a Protocol to describe a protocol parameter.

.. literalinclude:: _static/isajson/protocol_parameter_schema.json
    :language: json

**protocol_schema.json**

This schema implements Protocol from the ISA Abstract Model.

.. literalinclude:: _static/isajson/protocol_schema.json
    :language: json

**publication_schema.json**

This schema implements Publication from the ISA Abstract Model.

.. literalinclude:: _static/isajson/publication_schema.json
    :language: json

**sample_schema.json**

This schema implements Sample from the ISA Abstract Model.

.. literalinclude:: _static/isajson/sample_schema.json
    :language: json

**source_schema.json**

This schema implements Source from the ISA Abstract Model.

.. literalinclude:: _static/isajson/source_schema.json
    :language: json