In progress work to use NLP and SciGraph for mapping unstructured metadata key value pairs to ontologies.
With free text non-ontology keys, users can represent information in multiple ways. For instance, a key can have contextual information on the experiment nested within the keys:
ex485em528_raw,0.95
Or multiple keys representing the same information, with users needing to infer grouping based on their knowledge of the experiment:
Emission: ideal (nanometer),528
Excitation: ideal (nanometer),485
Value,0.95
Timepoint (second),10
To map keys to ontologies, specify a set of rules which define the inputs
and ontology terms. The input is pat, a regular expression that matches
to the existing key/value pair. The regular expression can include references
to other patterns to help retrieve embedded information in a key. To map to
ontologies, either specify a search term which SciGraph uses to retrieve
the ontology or a specific ontology reference. You can also specify a type
where it is difficult to infer from the input values themselves. The first
key value example above maps with these rules:
{:pat "^ex(?P<excitation>\d{3})em(?P<emission>\d{3})$" :search "fluorescence intensity" :type "float"}
{:pat "excitation" :ontology "BAO_0000566"}
{:pat "emission" :ontology "BAO_0000567"}
For the second multi-key example, group together separate keys using a
shared namespace, with the ns tag:
{:pat "excitation" :ontology "BAO_0000566" :ns "fluorescence"}
{:pat "emission" :ontology "BAO_0000567" :ns "fluorescence"}
{:pat "^value" :custom "value" :type "string" :ns "fluorescence"}
{:pat "^time(point)?$" :search "time measurement" :type "long" :ns "fluorescence"}
We ideally use OBO Foundry ontologies:
- Sequence Ontology (SO) -- description of sequence features in annotations
- Systems Biology Ontology (SBO)
- BioAssay Ontology (BAO) -- screening assays and results, not OBO but slimmer than NCIT
- The Ontology for Biomedical Investigations (OBI)
- Statistical Methods Ontology (STATO)
- Chemical Entities of Biological Interest (ChEBI)
- Metabalomics Standards Initiative Ontology (MSIO)
Other useful supplementary ontologies:
Useful tools:
Install data and tools:
bash get_data.sh
bash get_tools.sh
Load ontologies and run SciGraph server:
bash run_load.sh
bash run_service.sh
- Explore if OpenRefine helps over standard SciGraph queries