added more documentation as well as reformatted the files

docs/genome_annotation.rst

@@ -0,0 +1,75 @@
+.. _genome_annotation:
+
+Annotated Genome Data
+----------------------
+
+Overview
+.........
+
+Generate JSON-LD files for annotated genes from a given GFF3 file. Currently GFF3 files from ENSEMBL and NCBI are supported.
+
+Each JSON-LD file will contain:
+
+- GeneAnnotation objects
+- 1 GenomeAnnotation object
+- 1 GenomeAssembly object
+- 1 OrganismTaxon object
+- 1 Checksum object
+
+Command Line 
+.............
+
+``bkbit gff2jsonld``
+,,,,,,,,,,,,,,,,,,,,,
+
+    .. code-block:: bash
+
+        $ bkbit gff2jsonld [OPTIONS] GFF3_URL
+
+Options
+,,,,,,,,
+
+    ``-a, --assembly_accession``
+        ID assigned to the genomic assembly used in the GFF3 file.
+        **Note: Must be provided when using ENSEMBL GFF3 files**
+
+    ``-s, --assembly_strain``
+        Specific strain of the organism associated with the GFF3 file.
+
+    ``-l, --log_level``
+        Logging level.
+
+        Default:
+            WARNING
+        Options:
+            DEBUG | INFO | WARNING | ERROR | CRITICIAL
+
+    ``-f, --log_to_file``
+        Log to a file instead of the console.
+
+        Default:
+            FALSE
+
+Arguments
+,,,,,,,,,,,
+
+    ``GFF3_URL``
+        URL to the GFF3 file.
+
+Examples 
+.........
+
+Example 1: NCBI GFF3 file
+,,,,,,,,,,,,,,,,,,,,,,,,,,
+
+.. code-block:: bash
+
+    $ bkbit gff2jsonld 'https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9823/106/GCF_000003025.6_Sscrofa11.1/GCF_000003025.6_Sscrofa11.1_genomic.gff.gz' > output.jsonld
+
+
+Example 2: ENSEMBL GFF3 file
+,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
+
+.. code-block:: bash
+
+    $ bkbit gff2jsonld -a 'GCF_003339765.1' 'https://ftp.ensembl.org/pub/release-104/gff3/macaca_mulatta/Macaca_mulatta.Mmul_10.104.gff3.gz' > output.jsonld

docs/index.rst

@@ -14,22 +14,22 @@ This package contains tools to use the BICAN Knowledgebase Data Models.
    install
 
 .. toctree::
-   :maxdepth: 2
-   :caption: USAGE
+   :maxdepth: 4
+   :caption: DATA TRANSLATORS
 
-   data_translators
+   specimen_file_manifest
+   specimen_metadata
+   genome_annotation
 
 .. toctree::
    :maxdepth: 1
    :caption: REFERENCE
 
    modules
 
-
-
 Indices and tables
 ==================
 
 * :ref:`genindex`
 * :ref:`modindex`
-* :ref:`search`
+.. * :ref:`search`

docs/specimen_file_manifest.rst

@@ -0,0 +1,4 @@
+.. _specimen_file_manifest:
+
+Specimen File Manifest
+----------------------

docs/data_translators.rst → docs/specimen_metadata.rst

@@ -1,107 +1,55 @@
-.. _datatranslators:
+.. _specimen_metadata:
 
-Data Translators
-======
-
-Annotated Genome Data
+Specimen Metadata
 ----------------------
-Generate JSON-LD files for annotated genes from a given GFF3 file. Currently GFF3 files from ENSEMBL and NCBI are supported.
 
-Each JSON-LD file will contain:
+Overview
+.........
 
-- GeneAnnotation objects
-- 1 GenomeAnnotation object
-- 1 GenomeAssembly object
-- 1 OrganismTaxon object
-- 1 Checksum object
+Generate JSON-LD files for specimens, subjects, and their repective ancestors or descendants. Data is retrieved from the `BICAN Specimen Portal <https://brain-specimenportal.org/>`_. 
 
 Command Line 
 .............
 
-``bkbit gff2jsonld``
+``bkbit specimen2jsonld``
 ,,,,,,,,,,,,,,,,,,,,,
 
-    .. code-block:: bash
-
-        $ bkbit gff2jsonld [OPTIONS] GFF3_URL
-
-Options
-,,,,,,,,
-
-    ``-a, --assembly_accession``
-        ID assigned to the genomic assembly used in the GFF3 file.
-        **Note: Must be provided when using ENSEMBL GFF3 files**
-
-    ``-s, --assembly_strain``
-        Specific strain of the organism associated with the GFF3 file.
-
-    ``-l, --log_level``
-        Logging level.
-
-        Default:
-            WARNING
-        Options:
-            DEBUG | INFO | WARNING | ERROR | CRITICIAL
-
-    ``-f, --log_to_file``
-        Log to a file instead of the console.
-
-        Default:
-            FALSE
-
-Arguments
-,,,,,,,,
-
-    ``GFF3_URL``
-        URL to the GFF3 file.
-
-Examples 
-.........
-
-Example 1: NCBI GFF3 file
-,,,,,,,,,,,,,,,,,,,,,,,,,,
-
 .. code-block:: bash
 
-    $ bkbit gff2jsonld 'https://ftp.ncbi.nlm.nih.gov/genomes/all/annotation_releases/9823/106/GCF_000003025.6_Sscrofa11.1/GCF_000003025.6_Sscrofa11.1_genomic.gff.gz' > output.jsonld
-
+    $ bkbit specimen2jsonld [OPTIONS] NHASH_ID_OR_FILE
 
-Example 2: ENSEMBL GFF3 file
-,,,,,,,,,,,,,,,,,,,,,,,,,,,,,
-
-.. code-block:: bash
-
-    $ bkbit gff2jsonld -a 'GCF_003339765.1' 'https://ftp.ensembl.org/pub/release-104/gff3/macaca_mulatta/Macaca_mulatta.Mmul_10.104.gff3.gz' > output.jsonld
+**Options**
 
+    ``-d, --decendants``
+        A boolean flag that, when provided, generates BICAN objects for the given NHASH_ID and all of its descendants. 
+        If this flag is not set (DEFAULT), then the ancestors will be processed.
 
-Specimen Data
-----------------------
-Generate JSON-LD files for specimens, subjects, and their repective ancestors or descendants. Data is retrieved from the `BICAN Specimen Portal <https://brain-specimenportal.org/>`_. 
+**Arguments**
 
-Command Line 
-.............
+    ``NHASH_ID_OR_FILE``
+        The NHASH_ID of the specimen or a file containing a list of NHASH_IDs. 
+        If a file is provided, the file should contain one NHASH_ID per line.
 
-``bkbit specimen2jsonld``
+``filemanifest2jsonld``
 ,,,,,,,,,,,,,,,,,,,,,
 
-    .. code-block:: bash
+.. code-block:: bash
 
-        $ bkbit specimen2jsonld [OPTIONS] NHASH_ID_OR_FILE
+    $ bkbit specimen2jsonld [OPTIONS] NHASH_ID_OR_FILE
 
-Options
-,,,,,,,,
+**Options**
 
     ``-d, --decendants``
         A boolean flag that, when provided, generates BICAN objects for the given NHASH_ID and all of its descendants. 
         If this flag is not set (DEFAULT), then the ancestors will be processed.
 
-Arguments
-,,,,,,,,
+**Arguments**
 
     ``NHASH_ID_OR_FILE``
         The NHASH_ID of the specimen or a file containing a list of NHASH_IDs. 
         If a file is provided, the file should contain one NHASH_ID per line.
 
+
 Environment Variables 
 .............
 
@@ -174,8 +122,3 @@ Example 4: Parse a file containing record(s) and their respective descendants
     DO-WFFF3774.jsonld
     DO-RMRL6873.jsonld
 
-Structured Anatomical Data
-----------------------------
-
-
-