A utility library and set of command line tools for exchanging data in knowledge graphs.
The tooling here is partly generic but intended primarily for building the translator-knowledge-graph.
For additional background see the Translator Knowledge Graph Drive
The installation requires Python 3.
For convenience, make use of the venv module in Python 3 to create a lightweight virtual environment:
python3 -m venv env
source env/bin/activate
pip install -r requirements.txt
python setup.py install
The above script can be found in environment.sh
Use the --help flag with any command to view documentation. See the makefile for examples, and run them with:
make examples
The neo4j-upload command takes any number of input files, builds a networkx graph from them, and uploads that graph to a neo4j database. To do this it of course needs the database address, username, and password. This will only work through bolt. By default you can access a local neo4j instance at the address bolt://localhost:7687.
Usage: kgx neo4j-upload [OPTIONS] ADDRESS USERNAME PASSWORD INPUTS...
The --input-type option can be used to specify the format of these files: csv, ttl, json, txt, graphml, rq, tsv.
The neo4j-download command downloads a neo4j instance, builds a networkx graph from it, and saves it to the specified file. Like the upload command, this will only work through bolt.
Usage: kgx neo4j-download [OPTIONS] ADDRESS USERNAME PASSWORD OUTPUT
The --output-type option can be used to specify the format of these files: csv, ttl, json, txt, graphml, rq, tsv. The --labels and --properties options allow for filtering on node and edge labels and properties.
The labels filter takes two inputs. The first input is a choice of where to apply the filter: subject, object, edge, node. The second is the label to apply.
--labels edge causes
This will result in searching for triples of the form: (s)-[r:causes]-(o)
The properties filter takes three inputs: the first being a choice of where to apply the filter, the second being the name of the property, and the third being the value of the property.
--properties subject name FANC
This will result in searching for triples of the form: (s {name: "FANC"})-[r]-(o). These filter options can be given multiple times.
The --directed flag enforces the subject -> object edge direction.
The batch options allow you to download into multiple files. The --batch-size option determines the number of entries in each file, and the --batch-start determines which batch to start on.
The validate command loads any number of files into a graph and checks that they adhere to the TKG standard.
Usage: kgx validate [OPTIONS] INPUTS...
The --input-type option can be used to specify the format of these files: csv, ttl, json, txt, graphml, rq, tsv.
The dump command takes any number of input file paths (all with the same file format), and outputs a file in the desired format.
Usage: kgx dump [OPTIONS] INPUTS... OUTPUT
The format will be inferred from the file extention. But if this cannot be done then the --input-type and --output-type flags are useful to enforce a particular format. The following formats are supported: csv, tsv, txt (pipe delimited text), json, rq, graphml, ttl.
Note: CSV/TSV representation require two files, one that represents the vertex set and one for the edge set. JSON, TTL, and GRAPHML files represent a whole graph in a single file. For this reason when creating CSV/TSV representation we will zip the resulting files in a .tar file.
The dump command can also be used to relabel nodes. This is particularly useful for ensuring that the CURIE identifier of each node reflects its category (e.g. genes having NCBIGene identifiers, proteins having UNIPROT identifiers, and so on). The --mapping option can be used to apply a pre-loaded mapping to the output as it gets transformed. If the --preserve flag is used then the old labels will be preserved under a modified name. Mappings are loaded with the load-mapping command.
A mapping is just a python dict object. The load-mapping command builds a mapping out of the given CSV file, and saves it with the given name. That name can then be used with the dump commands --mapping option to apply the mapping.
Usage: kgx load-mapping [OPTIONS] NAME CSV
By default the command will treat the first and second columns as the input and output values for the mapping. But you can use the --columns option to specify which columns to use. The first and second integers provided will be the indexes of the input and output columns.
Note: the columns are zero indexed, so the first is 0 and the second is 1, and so on.
The --show flag can be used to display a slice of the mapping when it is loaded so that the user can see which columns have been used. The --no-header flag can be used to indicate that the given CSV file does not have a header. If this flag is used then the first row will be used, otherwise it will be ignored.
First we load a mapping from a CSV file.
$ kgx load-mapping --show --columns 0 1 a_to_b_mapping tests/resources/mapping/mapping.csv
a58 : b58
a77 : b77
a17 : b17
a28 : b28
a92 : b92
Mapping 'a_to_b_mapping' saved at /home/user/.config/translator_kgx/a_to_b_mapping.pkl
Then we apply this mapping with the dump command.
kgx dump --mapping a_to_b_mapping tests/resources/mapping/nodes.csv target/mapping-out.json
Performing mapping: a_to_b_mapping
File created at: target/mapping-out.json
The load-and-merge command loads nodes and edges from knowledge graphs as defined in a config YAML, and merges them into a single graph. The destination URI, username, and password can be set with the --destination-uri, --destination-username, --destination-password options.
Internal representation is networkx MultiDiGraph which is a property graph.
The structure of this graph is expected to conform to the tr-kg standard, briefly summarized here:
- Nodes
- id : required
- name : string
- category : string. broad high level type. Corresponds to label in neo4j
- extensible other properties, depending on
- Edges
- subject : required
- predicate : required
- object : required
- extensible other fields
Intended to support
- Generic Graph Formats
- local or remote files
- CSV
- TSV (such as the RKB adapted data loading formats)
- RDF (Monarch/OBAN style, ...)
- GraphML
- CX
- remote store via query API
- neo4j/bolt
- RDF
Neo4j implements property graphs out the box. However, some implementations use reification nodes. The transform should allow for de-reification.