pbuttigieg
commented
7 years ago @CommonClimate @VarshaKhodiyar
Hi Julien, many thanks for reaching out to us.
I am one of the originators of the LinkedEarth ontology, which currently focuses on the paleoclimate domain. I was steered in your direction by Varsha Khodiyar at Scientific Data, because apparently they can only use ontologies served by bioportal to describe their metadata records, and ENVO is the most proximate ontology to describe a large paleoclimate dataset. Unfortunately, it is lacking many concepts/terms that are essential in our field, so I was wondering if you would like to review it and adopt some of its terms: http://linked.earth/ontology/
We can certainly explore this - our domain is quite focused on environmental entities and their qualities (which are strongly linked to variables and data). Thus we may not be able to host all the terms within ENVO; however, we can try to broker terms to other compatible ontologies in the appropriate domains if needed.
The LiPD Ontology aims to provide a common vocabulary for annotating paleoclimatology data
We'd probably have to coordinate with the Information Artifact Ontology and the Relations Ontology ( @cmungall ) to integrate this content correctly, but I think this is doable. We have some starting points for variables (via the properties/qualities of environmental entities) and quite a few of the more general classes.
The Proxy Archive Ontology defines different types of proxy archives that we can find in a paleo climate dataset. (e.g. ice, marine sediments, corals, wood, etc)
This is very much in our domain and I think we actually have a lot of this content.
The Proxy Observation Type Ontology defines different types of proxy observations that we can find in a paleo climate dataset. (e.g. stable isotopes, trace metals, layer thickness, organic unsaturation index, etc).
These look like qualities of environmental data which we can integrate well.
The Proxy Sensor Ontology defines different types of proxy sensors that we can find in a paleo climate dataset. (e.g. trees, coral polyps, foraminifera, forest ecosystems, etc).
In some cases (forests, stands of trees, ...) ENVO is a good fit. For living organisms, you may want to ask if you can give a PURL to something in the ontologised version of NCBITaxon. We import classes from there when we want to handle organismal environments. For dead organisms or fossils, we could add material to ENVO too.
The Instrument Ontology defines the different types of instruments that can be used to measure in a paleo climate dataset. (this, in particular, could be applicable to a lot more than paleoclimatology).
This sounds like another external ontology. Devices have typically gone to OBI, which was initially about biomedical investigations, but has since expanded. We're musing about pitching the creation of a branch concerned with environmental sensors: perhaps this is a chance to consider this more seriously.
Inferred Variable Ontology describes a taxonomy of the most common types of inferred variables that can be found in a dataset. (I suspect this one won't be of too much use).
This is another point of contact with the IAO with links to ENVO classes.
Please let me know if any of these concepts could be useful to you, or if you would rather me list the concepts that we most urgently needed added to ENVO so we can properly describe our data with it.
I think we should definitely handle the urgent concepts first. This will give us a feeling of what needs to be done going forward. As always, we're happy to co-develop and align with external efforts. If you would be interested in leading a paleo branch of ENVO, please let us know.
CommonClimate
Hi, I am one of the originators of the LinkedEarth ontology, which currently focuses on the paleoclimate domain. I was steered in your direction by Varsha Khodiyar at Scientific Data, because apparently they can only use ontologies served by bioportal to describe their metadata records, and ENVO is the most proximate ontology to describe a large paleoclimate dataset. Unfortunately, it is lacking many concepts/terms that are essential in our field, so I was wondering if you would like to review it and adopt some of its terms: http://linked.earth/ontology/
It is made of 5 smaller ontologies:
Please let me know if any of these concepts could be useful to you, or if you would rather me list the concepts that we most urgently needed added to ENVO so we can properly describe our data with it.
Thanks in advance for considering, Julien