Feedback on the Status Update
So, on December 22nd I hosted a webinar to discuss the status update I had published on YouTube of ChAMP and gather feedback on what the attendees thought and what might be missing from the platform. The hour long discussion featured myself, Tony, and thirteen other attendees from various organizations.
In general, I got the feeling that the attendees thought there was a need for ChAMP, but that they needed to see it in action to fully understand the scope and usage.
Specific feedback was as follows
- Controlled vocabularies
- Look at MzML (Proteomic Standards Initiative) controlled vocabulary of terms for NMR
- Use cases
- Regulatory environment (FDA/SDD (Stability Data Standard), EPA/SEDD (Staged Electronic Data Deliverable) )
- Standard for Exchange of Nonclinical Data (SEND)
- IDMP (European)
- ISO 11615, Health informatics — Identification of medicinal products — Data elements and structures for the unique identification and exchange of regulated medicinal product information
ISO 11616, Health informatics — Identification of medicinal products — Data elements and structures for the unique identification and exchange of regulated pharmaceutical product information
ISO 11238, Health informatics — Identification of medicinal products — Data elements and structures for the unique identification and exchange of regulated information on substances
ISO 11239, Health informatics — Identification of medicinal products — Data elements and structures for the unique identification and exchange of regulated information on pharmaceutical dose forms, units of presentation, routes of administration and packaging
- ISO 11240, Health informatics — Identification of medicinal products — Data elements and structures for the unique identification and exchange of units of measurement.
- Chain of custody
- Who did something? (i.e. Regulatory environment needs personnel)
- Purpose? Why was this analysis done?
Looks like I have some additional work to do...
Where doe sthe time go? I am still thinking its August...well maybe i'm just holding on to the idea that I am 'just starting' my sabbatical. The reality is I am 9 weeks in and can't get over the idea that I am behind. Must be trying to do too many things and thus not getting many of them to completion. OK, October has to be more organized... [Ironically I am listening to 'Life in One Day' by Howard Jones as I write this...]
Anyway, I guess I should talk about what's happend on the ChAMP site this week :) Worked on the sample metadata (originally the matrix metadata) and moved some of the metadata from the sampleprep category into the sample category as I obviously fits better.
The Devil is in the Details
I just put up my first attempt at the analyte and sample preparation metadata. I am concerned that I have under-thought the analytes and over-thought the sample preparation. What I have put together seems to make sense to me, but I do not have an industrial, environmental, or government perspective on these areas and I imagine there are lots of changes to be made.
With that in mind I am going to do another social media blitz to get more people involved. Once things get rolling it will be OK, but I need to remove the current inertia to get there.
So, research takes three times longer than you think :( I knew that was true in the lab but I thought "I'm doing a computer based project, it can't take three times longer". Well it does. I just put up a first look at analytical metrics from the literature and I thought it would take me a day - it took three. Hopefully the other parts of that project will be shorter...
Also added the first version of the description category metadata. Wondering if it is enough to cover the bases. Probably I should put up a poll about this...
Looking at Google Analytics from the first week the website was up I am encouraged. 135 people came by and 18 people voted in the metrics poll. Still, I need to keep this on the radar... Interestingly, the highest percentage of views is from the UK and this is likely to increase as Serin Dabb helped get this into the latest Analyst issue as an eToc alert - thanks Serin.
So, my colleague at UNF, Bryan Knuckley, pointed out https://hootsuite.com as a possible solution to my social media lament of yesterday - thanks Bryan!
I keep finding interesting and useful sites such as
- Force11 (https://www.force11.org/) - "The future of research communications and e-scholarship"
Especially important are the Force11 data citation principles (https://www.force11.org/datacitationprinciples)
- FAIRport (https://www.datafairport.org/) - Find, Access, Interoperate, Re-use data approach
Import are the guiding principles (https://www.force11.org/group/fairgroup/fairprinciples)
OK, got to get some work done...
Down to Work
So, I have been all over social media to get the message out about ChAMP and I am pleased with the initial results. But, I get the feeling that if I don't keep constantly 'fanning the flames' as it were, the project will drop off the radar real quick. I guess rather than being controversial (and get folk all riled up) I will ask lots of questions via Twitter, ResearchGate and LinkedIn. Which leads me to a thought... Where is the app to allow me to write it once and send it out to all the streams? It's got be somewhere...
Anyway, I just put up the metadata structure poll after having fleshed out ten categories of info that seem to make logical sense to me. I hope folk give me some feedback on this...
I think another part of this project has led me to something else I feel I need to find and/or create - an ontology for numeric scientific data (ONSciD ?). By that I mean being able to annotate individual numeric data to describe the value, error, precision etc. (How nerdy is that?) Searching the web I found this which is interesting but not really what I am talking about. Posted a question on Twitter we will see what comes up (do I have to invent everything? :) )
[Aside... I did find an interesting article about ontologies while searching for ONSciD on what makes them useful.]
Ontologies and Guidelines for Data and Units
Going through the (old) Open PHACTS (https://web.archive.org/web/20190127095843/http://www.openphacts.org/) website I just found some more great resources for this project:
- Encoding Units and Unit Types in RDF (https://web.archive.org/web/20150912011738/http://www.openphacts.org/specs/2013/WD-units-20130913/)
- Guidelines for Exposing Data as RDF (https://web.archive.org/web/20150910133201/http://www.openphacts.org/specs/2013/WD-rdfguide-20131007/)
- QUDT - Quantities, Units, Dimensions and Data Types Ontologies (http://www.qudt.org/)
- Ontology of Units of Measurement (http://www.obofoundry.org/ontology/uo.html)
If only the guys developing SWEET (https://github.com/ESIPFed/sweet) and those developing QUDT at NASA could join forces with NIST and UnitsML (https://unitsml.nist.gov/) then we could have something definitive... (as of 12/1/20 there is something brewing at https://www.bipm.org/en/committees/cc/wg/cipm-tgdsi.html)
3, 2, 1 Launch!
Finally got the site to where I wanted it for the official launch. Already sent out an announcement via the ACS Analytical facebook page and the RSC and now I need to start working social media land.
I have no idea how much interest/participation I am going to get, but whatever happens I am going to have fun working on this project.
The ChAMP Website is Born...
So, the ChAMP website is born. Just like a newborn child I'm not sure what it will evolve into exactly, but I sure hope that it galvanizes people around the idea of developed a framework for analytical method metadata. I still have a lot of pages to write, but as I work on it I am having some good ideas of resources to add.
This entry is posted on an install of Joomla 3.3 with JCE (text editor) and Kunena (bulletin board).
More to follow before I release to the world.