NOTE: this is the new version of the repository at https://bitbucket.org/petermr/xhtml2stm/wiki/Home.
AMI provides a generic infrastructure where plugins can search, index or transform structured documents on a high-through basis. The typical input is structured, normalized, tagged XHTML, possibly containing (or linked to) SVG and PNG files. The plugins are designed to analyse text or graphics or a combination according to the discipline.
AMI has been through 2 major revisions, and most recently has been split into two parts (a) Norma which processes legacy documents and normalizes HTML (NHTML) and (b) AMI which runs plugins over the NHTML. AMI currently processes PDF, XML, HTML, etc but these will be obsoleted in favour of the output from Norma.
AMI has a plugin architecture where each problem or community has its own plugin. Examples are "species", "sequence", "regex" and soon some chemistry.
It is often straightforward to develop text-based searches, and this is accessible to most committed scientists. Graphics is always harder and requires bespoke programming. Plugins have been developed for at least:
- indexing text by regular expressions (
regex). - Genbank IDs
- PDB ids
- farm-related / agronomy terms
- chemical species (OSCAR)
- computational phylogenetics
- terms identifying Ebola and other haemorrhagic diseases
- phylogenetic trees
- chemical structures
The plugin architecture is moderately stable and it requires very little alteration to the codebase to add a new one (hopefully soon this can be done automatically by configuration files).
The input must be a QuickscrapeNorma directory (QSNorma). This must contain scholarly.html which is used for
analysis. When a plugin is run, the output is to the results directory, wiwth a subdirectory for each plugin
and a sub-subdirectory for each plugin option: Example:
http_www.foo_1_2/
fulltext.xml
fulltext.pdf
scholarly.html
results/
words/
frequency/
results.xml
lengths/
results.xml
regex/
consort0/
results.xml
publication/
results.xml