To setup ZOOMA, download the latest release from here and extract the archive (tar.gz or zip, depending on your platform or which version you chose) to your desired location.
ZOOMA requires several configuration files, which you may not need to edit for basic functionality but can be tailored to suit your purposes. These files are located in the config/ directory beneath the root directory.
The ZOOMA application directory should be laid out as below:
zooma/
|-- bin/
| |-- zooma
| `-- zooma.bat
|-- config/
| |-- log4j.xml
| |-- default-ontologies-config.properties
| |-- default-rejected-ontologies-config.properties
| |-- default-sources-config.properties
| `-- zooma-uris.properties
`-- lib/
`-- ...many required java dependencies
Scripts for invoking ZOOMA on the command line are located in the bin/ directory - zooma for unix based platforms, including MAC, and zooma.bat for windows systems. You might want to add this location to your path.
Java jar files required for the operation of ZOOMA are located in the lib/ directory
You can tailor the operation of ZOOMA by editing the files in the config/ directory to suit your requirements. If you want to adjust ZOOMA's behaviour, you should read the description of each of these files, outlined below.
ZOOMA works by looking for best ontology matches. A good deal of this involves ranking various sources or ontologies against one another, in preference order. The files "default-sources-config.properties" and "default-ontologies-config.properties" define these rankings.
This file defines the sources that you prefer mappings to come from. ZOOMA uses a variety of sources to fetch candidate mappings - any resource that can be searched for ontology terms 'matching' a given text value can be considered as a repository of ontology mappings.
This file is simply used to rank these sources in preference order. Mappings from preferred sources will be ranked higher than those from other sources.
To declare you rankings, simply name each source in turn. Allowed sources currently are:
ARRAYEXPRESS2, ATLAS, EFO, OWL, MAGETAB, ONTOCAT, OLS_VIA_ONTOCAT, BIOPORTAL_VIA_ONTOCAT, OLS, BIOPORTAL, USER_DESCRIBED, AGGREGATED_SOURCE, OTHER_SOURCE
...but this list can be extended to suit your requirements.
This file defines the ontologies that you prefer. ZOOMA will rank mappings from preferred ontologies above those from others. Also, by default a preferred ontology trumps a preferred source: so if you have a mapping to a preferred ontology from a less preferred source, and a mapping to a less preferred ontology from a more preferred source, the first mapping is considered to be better.
In addition, this file provides some integration between disparate ontology mapping repositories. Within this file, you must declare a name that ZOOMA will use to uniquely identify each ontology, followed by a comma separated list of aliases. The unique name should not contain the characters '=' or ':', and it is a good idea to use the same name as that declared in the file zooma-uris.properties (see below).
ZOOMA uses this mapping internally to collapse hits from these ontologies into one. Take a look inside this file to see some examples of how this is done. Note that the fact that an ontology is absent from this file does NOT mean ZOOMA will never map to this ontology - it just means it will prefer mappings to others mentioned first. To specifically exclude an ontology, you must add a line to the file "default-rejected-ontologies-config.properties"
This file defines any ontologies that should NEVER be mapped to. Any hits to these ontologies will automatically be rejected by ZOOMA, regardless of any other information on rankings and irrespective of whether any other hits occur.
The file "zooma-uris.properties" declares the logical URI of any ontology, where available. Not all things known as ontologies utilise these URIs the same way - OWL ontologies will usually have a logical URI, and often this will be resolvable from the matching URL, but this is rarely the case for OBO ontologies.
However, this file declares the URIs, wherever they are available, of ontologies and important concepts within that ontology (the URI of the superclass of all obsolete classes, for example). These can then be used by ZOOMA to add extra value to mappings (in this example, by excluding mappings to obsolete terms).