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.
There are binaries provided with releases which enable running of ami's plugins; shell and batch scripts are provided to make running these easier. Detailed tutorials of these can be found in the ContentMine software tutorials.
Run on a CTree which contains scholarly.html files of the papers you are analysing. This can be made using Norma.
ami2-gene --project zika --g.gene --g.type human
After the build, shell scripts and batch files to run plugins are in
target/appassembler/bin/. Further documentation is in
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 (
- 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