Giuseppe Totaro created TIKA-1580:
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Summary: ISA-Tab
Key: TIKA-1580
URL: https://issues.apache.org/jira/browse/TIKA-1580
Project: Tika
Issue Type: New Feature
Components: parser
Reporter: Giuseppe Totaro
Priority: Minor
We are going to add parsers for ISA-Tab data formats.
ISA-Tab files are related to [ISA Tools|http://www.isa-tools.org/] which help
to manage an increasingly diverse set of life science, environmental and
biomedical experiments that employing one or a combination of technologies.
The ISA tools are built upon _Investigation_, _Study_, and _Assay_ tabular
format. Therefore, ISA-Tab data format includes three types of file:
Investigation file ({{a_xxxx.txt}}), Study file ({{s_xxxx.txt}}), Assay file
({{a_xxxx.txt}}). These files are organized as [top-down
hierarchy|http://www.isa-tools.org/format/specification/]: An Investigation
file includes one or more Study files: each Study files includes one or more
Assay files.
Essentially, the Investigation files contains high-level information about the
related study, so it provides only metadata about ISA-Tab files.
More details on file format specification are [available
online|http://isatab.sourceforge.net/docs/ISA-TAB_release-candidate-1_v1.0_24nov08.pdf].
The patch in attachment provides a preliminary version of ISA-Tab parsers
(there are three parsers; one parser for each ISA-Tab filetype):
* {{ISATabInvestigationParser.java}}: parses Investigation files. It extracts
only metadata.
* {{ISATabStudyParser.java}}: parses Study files.
* {{ISATabAssayParser.java}}: parses Assay files.
The most important improvements are:
* Combine these three parsers in order to parse an ISArchive
* Provide a better mapping of both study and assay data on XHML. Currently,
{{ISATabStudyParser}} and {{ISATabAssayParser}} provide a naive mapping
function relying on [Apache Commons
CSV|https://commons.apache.org/proper/commons-csv/].
Thanks for supporting me on this work [~chrismattmann].
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