Open Microscopy Environment

Hi All,

Since I am new to this group, I would like to first introduce myself: my name is Paulo Pinheiro (http://paulopinheiro.info) and I am a staff scientist (computer scientist) at Pacific Northwest National Laboratory.

I have seen that OME metadata has been encoded in XML schema. I would like to know if someone has an OWL ontology built on top of XSD. Also, I would like to know if the group has discussed the possibility of reusing ontologies/vocabulary schemas rather than building everything inside of a single convention.

Finally, I have the impression that the microscopy environment of concern behind OME is more in support of biology. I will be glad to know that my impression is incorrect and to know more about how your conventions support TEM/DTEM observations in the areas of chemistry and material sciences.

Many thanks,
Paulo.

pinheiro wrote:Since I am new to this group, I would like to first introduce myself: my name is Paulo Pinheiro (http://paulopinheiro.info) and I am a staff scientist (computer scientist) at Pacific Northwest National Laboratory.

Hi Paulo,

pinheiro wrote:I have seen that OME metadata has been encoded in XML schema. I would like to know if someone has an OWL ontology built on top of XSD.

There was a previous effort in Australia to map an older version of the schema to OWL. The OME project itself, however, does not currently maintain an OWL version of the schema.

pinheiro wrote:Also, I would like to know if the group has discussed the possibility of reusing ontologies/vocabulary schemas rather than building everything inside of a single convention.

We are certainly interested in interoperating with existing standards where possible by allowing users to link in an RDF-like manner out to external terms. What particular use case were you thinking about?

pinheiro wrote:Finally, I have the impression that the microscopy environment of concern behind OME is more in support of biology. I will be glad to know that my impression is incorrect and to know more about how your conventions support TEM/DTEM observations in the areas of chemistry and material sciences.

The OME schema is very much in the biological/medical domain, and the core team has no particular expertise in other domains. This doesn't mean that we wouldn't be interested in hearing suggestions for how the schema specification could be modified to work in other domains, just that we can't drive that effort.

Best wishes,
~Josh.