Monthly Archives: June 2012

Swopulous: SWOP meets Populous

To make it easier to describe software we have created an Excel spreadsheet using the tool Populous which is based on another tool called RightField [1]. The spreadsheet is available for download here. References Wolstencroft K, Owen S, Horridge M, Krebs O, … Continue reading

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Links between data formats

This modification to SWO came out of a problem very similar to the one recently described for linking two pieces of software together. Rather than linking two pieces of software, here we would like to relate different data format specification … Continue reading

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Links between software

Until now, SWO had only one way of linking software to each other: via the defined class Software Suite, which has as its equivalent class has_part some software. This has the benefits of being straightforward and also quite useful for … Continue reading

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Adding a Web interface

With the large number of browser-based applications available, a new class within Software interface was needed. Prior to this change, there were four classes under Software interface: Graphical User Interface, Application Programming Interface, Command Line Interface and Web Service. What … Continue reading

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Versioning in SWO

Recently we noticed that version information was stored as instance data of the ‘version name or number’ class. A few of us asked each other what the gain was in having instance data rather than simple string values on the … Continue reading

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Merging two SBML data format classes

As I was investigating the data formats in swo_data.owl I noticed that there were two classes that overlapped: SBML and SBML file. Both of these classes were present as children of data format specification. Perhaps the original intention of SBML … Continue reading

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The Third Software Ontology Workshop

Agenda As with the previous two workshops, we’ll actually be doing work. we have the following objectives: Adding software to the sWO; Using Populous and rightField to annotate software with the SWO and add it to the SWO; review the … Continue reading

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Clustal and other MSA tools

Clustal There are two versions of Clustal produced by its authors: Clustal 2 (also called ClustalW2) and Clustal Omega. Both provide multiple sequence alignment, although Clustal Omega currently only works on protein sequences (www.clustal.org). Clustal Omega has a publication at … Continue reading

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Tidying up annotation labels

As I have begun to start adding software in earnest, I have noticed some duplication of intent (and one straight duplication) within the annotation labels used in SWO. As such, the following tidying up of annotation labels has been completed: … Continue reading

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Updates and additions to the BLAST software class

The initial goal of all of the software I’m going to be adding over the next few weeks is to model function, then to go back and model inputs and outputs. As there is time, further modelling (e.g. organizations involved, … Continue reading

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