Add integer and identifiers to node metadata

[callahantiff]

Problem: Right now the node metadata that is output is keyed by an identifier, which means if you use the integer edge lists, but want node labels you have to use the provided dictionary that maps node integers to identifiers first.

Solution: In the next iteration, I will add a new column that includes the identifier and the integer. Examples of each output are shown below.

An example of the current output: node_id	label	description/definition	synonym
388324	INCA1	INCA1 has locus group 'protein-coding' and is located on chromosome 17 (map_location: 17p13.2).	HSD45protein INCA1
92106	OXNAD1	OXNAD1 has locus group 'protein-coding' and is located on chromosome 3 (map_location: 3p25.1-p24.3).	oxidoreductase NAD-binding domain-containing protein 1
56140	PCDHA8	PCDHA8 has locus group 'protein-coding' and is located on chromosome 5 (map_location: 5q31.3).	PCDH-ALPHA8protocadherin alpha-8	KIAA0345-like 6	PCDH-alpha-8

An example of the improved output: node_integer	node_id	label	description/definition	synonym
0	388324	INCA1	INCA1 has locus group 'protein-coding' and is located on chromosome 17 (map_location: 17p13.2).	HSD45protein INCA1
1	92106	OXNAD1	OXNAD1 has locus group 'protein-coding' and is located on chromosome 3 (map_location: 3p25.1-p24.3).	oxidoreductase NAD-binding domain-containing protein 1
2	56140	PCDHA8	PCDHA8 has locus group 'protein-coding' and is located on chromosome 5 (map_location: 5q31.3).	PCDH-ALPHA8protocadherin alpha-8	KIAA0345-like 6	PCDH-alpha-8

[callahantiff]

• [x] Add relation information to metadata file. Will require a simple helper method to parse the graph and obtain relation labels

[callahantiff]

Verify node identifiers in output metadata, formatting for ensemble transcripts looks a bit off

[callahantiff]

• [x] weird content in output file, need to verify output form ontologies against new edges we add to isolate bug.
• [ ] Also want to think critically about how to add dbxrefs. May not be for v2.0.0, but I think adding this information will increase the usability of the result KG and make it easier for people to extend the KG with new data sources

[callahantiff]

• [ ] Export a dictionary for each node in the KG that contains two inner keys (i.e. edge type and node type) that can be used as a high-level way to organize the output data. This should be VERY simple to create for all builds.

A brief example of what this would like for node identifier rs201492213 is shown below:

node_type = 'variant' edge_type = ['variant-phenotype', 'variant-gene']

[callahantiff]

TASK

Task Type: CODEBASE

Improve the output metadata for nodes and edges in the knowledge graph

TODO

The following items have been condensed from the issues above.

• [x] Add a new column that includes the identifier and the integer (example shown here)
• [x] Add relation information to metadata file. Will require a simple helper method to parse the graph and obtain relation labels
• [x] Verify output form ontologies against new edges we add to isolate bug
• [x] Also want to think critically about how to add dbxrefs. May not be for v2.0.0, but I think adding this information will increase the usability of the result KG and make it easier for people to extend the KG with new data sources
• [x] Export a dictionary for each node in the KG that contains two inner keys (i.e. edge type and node type) that can be used as a high-level way to organize the output data. This should be VERY simple to create for all builds
• [x] Should be able to work with metadata abstracted from the merged ontologies

[callahantiff]

Done as part of #84