CleanUpDec07

Summary of the Instrument Branch Clean Up

• • Terms remaining to be cleaned:

• hybridization_chamber->to keep?cf below
• hybridization_station->to keep?cf below
• liquid_handler-> to keep? see below

• microarray_wash_station -> definition question, see below.
• crosslinking_instrument -> concerns about the term name, see below.
• FACS_Caliber -> concerns below

• SomaScope

• power_pack
• liquid_chromatography_instrument

Issues/Ideas

MC, 13/12/07

Did somebody remove some of the curation_status annotations? All terms had one added automatically and now some are missing. This is a required metadata as explained here https://wiki.cbil.upenn.edu/obiwiki/index.php/MinimalMetadata

(please add your initials to keep track of who suggested what)

AL, 11/12/07

• liquid_handler-> to keep? We already have notes in this term about keeping it only as a defined class, and infer children of it. I've cleaned up the definition, but there's not much else I can do until it is resolved.->FG will send an email to X in MO to sort that out

• microarray_wash_station: the current definition is "A microarray wash station is an instrument used to wash Affymetrix-type arrays.". Either this definition should be made more generic, or the term should be made more specific. It seems odd that such a general term as "microarray_wash_station" should be Affy-specific, doesn't it?->FG will send an email to X in MO to sort that out

• crosslinking_instrument: if we intend that other ontologies can be used in conjunction with OBI, we shouldn't have such a general term used specifically for chemically joining two or more molecules. I'm sure there are other "crosslinkers" that are on a much different scale in engineering etc. I have moved the original label to be an alternative term, and have renamed the main label accordingly (to molecular_crosslinker). Do you agree?->FG will send an email to X in MO to sort that out

MC,6/12/07

• OBI_IDs: should be 6 digits. This should probably be added to the Naming conventions page? We also should probably keep in mind to check that at some point.

DS: Yes should all be uniform. ID conventions are listed as part of the OBO policies on the wiki.

• polystyrene_tube (alt_term scintilliation_tube) should probably be tube with additional properties?

DS: If this is a frequently used entry term/search attribute we can have it as is I guess.

• filtration_labware: should probably be labware with a role of filtration?
• paper_filter -> shall we keep it?

DS: I guess yes. Why shouldn't we?

MC: sorry was unclear. do we want to list all the possible material filters can be made of? I am also thinking about things like "quartz cuvette". Is there a way in OBI to say a filter made of paper for example? a cuvette made of quartz? -> we keep at the moment and will see depending on the needs

• supernatant_collection_system_harvesting_frame -> I don't know what that is

DS: google harvesting frame supernatant -->

"The Supernatant Collection system is designed for collecting 90% of the supernatant in a microplate well and separating the living cell with no stress, eliminating centrifugation and other similar techniques. It can be used in a variety of release assays with different radioactive isotopes, such as Cr51 or I125.

The Supernatant Collection system offers a safe way to handle samples containing isotopes, and is being used in cytotoxicity testing for measurement of toxic effects on cellular material and chromium release studies. By eliminating tedious centrifuging and pipetting steps in these assays, the Supernatant Collection system offers a faster, safer, and more reproducible technique, producing more reliable results. In 1978, the Supernatant Collection system was added to the National Institute of Health's (NIH) Manual of Tissue Typing Tests. "

MC: should be supernatant_collection_system then, with the different parts of: http://www.moleculardevices.com/pages/instruments/scs1.html

• labware: hard to make the difference between labware/instrument. I didn't find a definition for labware, apart from "The term “labware” refers to tube racks, plate holders and other. equipment..". In my mind labware is the "small stuff" (not a definition!) and instrument the "big stuff", but the current definiton of instrument would also apply to labware:"An instrument is a device which provides a mechanical or electronic advantage as a participant in a process".

DS: Labware in of more primitive constitution, has less parts, is more passive than active....

In addition, heated_bath is under labware currently, why would it be there whereas centrifuge for example is under instrument.

-> labware is not top-priority at the moment

FG (7/12/07) comment: As described in the annotation properties of Labware it is only a placeholder at the minute for things that are not instruments. The whole object hierarchy is under review at the moment so the separation is temporary, indicated by the annotation property "graph_position_temporary". For the short term please ignore everything under labware and just deal with instruments. I agree the definition is not great but is dependent on a re-working of the object hierarchy.

MC (7/12/07): ok with that. I would suggest finishing the terms clean-up and our next action item could then be finalizing the hierarchy (labware, cardinal_part_of_ and _temporary)

MC,7/12/07

• difference between somacount and somascope?

MC, 10/12/07

• definition_citation: the cardinality of the definition_citation is 1, when there are 2 sources, do we put the 2 sources in the one field (separator?) or do we choose one?

Solved issues

• A10-Analyzer: I kept the hyphen as it is the instrument's name.

DS: Good.

• thermal_cycler: alternative terms PCR_machine. As per Daniels reccomendation I put PCR and Polymerase CHain Reaction _machine as alt terms. However an other alt term is DNA_amplifier, do we want to "explode" DNA?

No DNA is known in everyday language, see naming conventions.

• Guava cytometers use aspiration and not a fluid to transport the cells within the machine, however our definition of flow_cytometer says "A flow_cytometer is an instrument for counting, examining and sorting microscopic particles suspended in a stream of fluid"-> change to particle in suspension

• General question: Kevin C made the original definition of fluorometer, and I added to it. What should I put down as the editor? I've put in OBI, but I am unsure. Is it the person who last modified it?-> we put both in this case, Kevin and Allyson, in 2 annotations definition_editor

• FACS_Caliber: I haven't changed this at all, as I don't know much about cytometers, but I also know that "The FACS Calibur is one of the most popular cytometers in use for research]" isn't a good-enough definition! Ideas?->will be manufacturer and model number and use relations.

• FACSCalibur is an analyser and sorter. Should be moved under flow_cytometer_sorter?-> Daniel did it

• computer: current def says "is an electronic instrument". should "electronic" be submitted somewhere else? -> work on computer definition (Melanie)

• hybridization_chamber and station: hybridization should be a role?-> hybridization is a process

• ImageStream: is an image_cytometer AND flow_cytometer-> moved under instrument and has_part FC and has_part image_cytometer, child of the new class Multispectral Imaging Flow Cytometer
• Lactoscope is a spectrophotometer -> done

FG, (email 10/12/07)

Currently we intend to use the part of relation to describe the components parts of instruments. Due to this the "cardinal_part_of_instrument" class now seems out of place which is not even classified as a device. In addition I am not sure why there is a class called InstrumentAndPart_temporary within the hierarchy, also not asserted under device. If these RU's which are sublcasses of both cardinal_part_of_instrument and instumentAndPart_temporary are actually required in OBI then they should be modeled within the branch appropraitely. If they are not required they should be deleted.

If the RU are terms that have been submitted and required by OBI then I propose to place the RU in a class called UnassertedInstrumentAndPartRepresentationalUnit (or something similar) as a child of the instrument class.

In addition the class labelled "_move_to_biomaterial_branch" would appear to contain roles rather than biomaterials

The labware class currently exists only as a placeholder for devices that are not instruments. Therefore every child of labware should really just be asserted as a flat list. The class "filtration_labware" seems to have been arbitrarily added and would seem to conflate the role a particular entity of labware would perform. I would propose removing this class to maintin the flat list.