iRefIndex MITAB2.6 Parser
A tool has been developed to parse the MITAB files produced in the iRefIndex Build Process. Currently, the tool is capable of parsing the MITAB format described on the page README MITAB2.6 for iRefIndex.
Contents
Obtaining the MITAB Parser
The parser and associated resources are available for download here:
- Snapshot 2011-11-29: tar.bz2 archive, tar.gz archive, zip archive
- mitab repository home
Prerequisites
The following programs are required to use the parser:
- Python (tested with 2.5.4)
- PostgreSQL (tested with 8.1.17, 9.0.4)
Running the Parser
Given a directory for the iRefIndex output files such as...
/home/irefindex/output
...run the parser as follows:
python parse_mitab.py /home/irefindex/output/All.mitab.03042009.txt
It will be necessary to change the date details included in the above filename to match the actual name of the appropriate file found in your own output directory.
Creating the Database
A database can be created using the usual PostgreSQL tools:
createdb -E unicode mitab_irefindex
This database is initialised as follows:
psql -f init_mitab.sql mitab_irefindex
Should the database tables need to be dropped (perhaps in case of problems with the import), the following command can be used:
psql -f drop_mitab.sql mitab_irefindex
Populating the Database
The database is populated as follows:
python database_action.py mitab_irefindex import_mitab.sql
As a result, a number of tables representing the structure of the data should be available in the database. For applications built to use this data, indexes may need creating in order to make querying more efficient.
Notes on the Populated Database
The schema used by the populated database attempts to model the data as effectively as possible using a number of tables:
| Entity type | Tables | Table purpose | Notable columns | Source columns (if different or converted) |
|---|---|---|---|---|
| Interaction | mitab_interactions | Model each interaction referencing interactors | rigid, edgetype, numParticipants, crigid | |
| mitab_sources | Represent sources for each interaction | rigid, sourcedb, name | sourcedb | |
| mitab_interaction_type_names | Represent interaction types for each interaction | rigid, code, name | interactionType | |
| mitab_interaction_identifiers | Represent interaction identifiers for each interaction | rigid, dbname, uid | interactionIdentifiers | |
| mitab_confidence | Represent confidence scores for each interaction | rigid, type, confidence | confidence | |
| mitab_interaction_rigs | Represent alternative integer identifiers for each interaction | uid, rig | rigid, irigid | |
| Canonical interaction | mitab_canonical_interaction_rigs | Represent alternative integer identifiers for each canonical interaction | uid, rig | crigid, icrigid |
| Experiment | mitab_method_names | Represent detection methods for each interaction | rigid, code, name | method |
| mitab_authors | Represent publication authors for each interaction | rigid, author | author | |
| mitab_pubmed | Represent publication identifiers for each interaction | rigid, pmid | pmids | |
| Interactor | mitab_interactions | Model each interaction referencing interactors | uidA, uidB, taxA, taxB, atype, btype, crogidA, crogidB | |
| mitab_aliases | Represent aliases for each interactor | uid, dbname, alias | uidA or uidB, aliasA or aliasB | |
| mitab_alternatives | Represent alternative identifiers for each interactor | uid, dbname, alt | uidA or uidB, altA or altB | |
| mitab_interactor_rogs | Represent alternative integer identifiers for each interactor | uid, rog | uidA or uidB, irogA or irogB | |
| Canonical interactor | mitab_canonical_interactor_rogs | Represent alternative integer identifiers for each canonical interactor | uid, rog | crogidA or crogidB, icrogA or icrogB |
Some changes in representation occur when creating the database:
- Prefixed values are generally split to expose the prefix and identifier, name or value following it.
- The various interaction and interactor prefixes (such as irefindex:, rigid:, rogid:, crigid: and crogid:) are omitted from interaction and interactor columns. Note that for non-iRefIndex data, any prefixes other than these will be retained, although this approach may be revised in future.
- Source identifiers are split with the prefix (such as intact:) used to make a dbname column with the actual identifier stored in its own column (such as alias or alt).
- The "empty value" (-) should never appear as an identifier, and where such a value is used in a list, that element should be excluded. This is pertinent in the case of vocabulary terms where MI:0000 might be used together with an empty list of identifiers or names as an "empty collection" indicator.
- Duplicate values in lists are generally discarded.
Further work may include the introduction of a separate interactor table, collecting related information for each interactor. Support for interactor identifiers other than ROG identifiers may be improved, with a new column potentially being introduced to indicate the type of each identifier.
Canonical interactors and interactions
The mitab_interactions table incorporates the canonical interaction and interactors alongside the specific interaction and interactors. A separate mitab_canonical_interactor_rogs table is used to map canonical interactors to integer identifiers, just as mitab_interactor_rogs does so for specific interactors.
All iRefIndex Pages
Follow this link for a listing of all iRefIndex related pages (archived and current).
