Species Code List

[mkm1879]

I believe we really need to expand the species list to include at least the full range of USDA three letter codes.

We are working on using the standard to file CVIs in USAHERDS. It is clear that the standard list will never include all the subdivisions that an application might support but it should at least have a parent of any given group. If I remember the discussion correctly, we had planned to revisit this list at some time anyway and just never got to it.

[mmcgrath]

Good morning Mike good idea - looks like the existing simpleType supports 7 options all of which happen to be three letter codes. Can you cut & paste the standard list in here as a comment to this issue? I'll then amend the schema and push the revised version for the group to review. If we're in agreement, we can ask USAHA to update the published version on their website.

Thanks Michael.

[mkm1879]

Yeah! That is a big part of the issue. The one thing I was really disappointed about our first effort was we never systematically evaluated our terminology. Species is the classic example. There is no good standard list. (Well except what that Swedish guy started way back when.) We clearly need to address things like small animals for some states, poultry for others, etc.

Here are three versions of the USDA codes to choose from:

From Animal Disease Traceability Technical Standards Document: AQU Aquaculture AVI Avian BEF Beef BIS Bison BOV Bovine (Bison and Cattle) CAM Camelid (Alpacas, Llamas, etc.) CAP Caprine (Goats) CER Cervids CHI Chickens CLM Clams CRA Crawfish CTF Catfish DAI Dairy DEE Deer DUC Ducks ELK Elk EQU Equine (Horses, Mules, Donkeys, Burros) GEE Geese GUI Guineas MSL Mussels OVI Ovine (Sheep) OYS Oysters POR Porcine (Swine) QUA Quail RTT Ratites (Emus, Ostriches, etc.) SAL Salmon SBA Striped Bass SHR Shrimp SLP Scallops TIL Tilapia TRO Trout TUR Turkeys

From The USDA Data Concepts Paper: Name Code Bovine BOV Caprine CAP Equine EQU Ovine OVI Porcine POR Poultry POU

From GDB (Snapshot of SC instance shortly before cutoff) Code Species AQU Aquaculture BOV Bovine (Bison and Cattle) CAM Camelid (Alpaca & Llama) CAP Caprine (Goats) CER Cervids CHI Chickens CLM Clams CRA Crawfish CTF Catfish DEE Deer DUC Ducks ELK Elk EMU Emu EQU Equine (Horses) GEE Geese GUI Guineas LAG Rabbits (Lagomorphs) MLT Multiple Non-livestock Species MSL Mussels OTH Other OVI Ovine (Sheep) OYS Oysters PET Pets Not Listed PGN Pigeon PHE Pheasants POR Porcine (Swine) POU Poultry QUA Quail RTT Ratites SAL Salmon SBA Striped Bass SHR Shrimp SLP Scallops SM Small Animals (Rabbits, etc.) TIL Tilapia TRO Trout TUR Turkeys WLD Wildlife Not Listed

[mmcgrath]

Shall we go for the ADT Tech Standards list?

[mkm1879]

That list would work here. We don't really do much with small animal certificates here in SC, but some states do, so I suspect we need to add codes for those. Our GDB had PET and SM. I'm not sure that is what we want either though.

Would Sara or someone who pays attention to small animal CVIs want to comment?

[sahola]

Sounds good to me. We don't do much with small animals either.

CAN Canine FEL Feline

then - other can fit for anything else

[mkm1879]

At this point, we don't even have Other, if I remember right. I think we need that.

[StaceySchwabenlander]

I like the addition of CAN and FEL, along with OTH (other) as suggested above. I would like to see small animal included so that we can be inclusive and not prohibit CVIs issued by small animal or mixed animal practitioners from utilizing this schema if the involved entities would find that beneficial.

[aeischeid]

At GlobalVetLink we collect Species and SpeciesType, I wonder if some adoption of a similar distinction would be helpful for this document. I just feels really odd to have Beef, Bison, Bovine, and Dairy as 'species' maybe it should not be called species, but something without a distinct meaning like 'animalType' if these are the the codes that need to be accepted for whatever reason.

[mkm1879]

As I see it, there are essentially two options. The first one is as you suggest to break “Beef Cattle” down into individual elements that each hold one fact. Species + Production Class to use HL7 names for them or Species + Species Type as you do. But what other elements

Another interesting approach takes much more sophisticated modeling to put all the facts about an animal, its age group, reproductive status, use, etc. in one ontology. Such an ontology was developed by the committee’s own Suzanne Santamaria.

http://scholar.lib.vt.edu/theses/available/etd-05082012-121749/unrestricted/Santamaria_SL_T_2012.pdf

This work has also proved useful when trying to do things like list standard age classes such as is done in the SECD response where they break down cases into Sow, nursery, feeder, etc.

For simple use cases like CVIs, two elements is probably the easier approach to implement.

Mike

Michael K. Martin, DVM, MPH, DACVPM Clemson Livestock Poultry Health PO Box 102406 Columbia, SC 29224-2406 email: mmarti5@clemson.edumailto:mmarti5@clemson.edu (If you ever don’t get a response, please try my personal email. The above works most of the time.) personal email: michael.martin.dvm.mph@gmail.com phone: (803) 788-2260 direct line: (803) 726-7808 work cell: (803)312-1439 personal cell: (803)348-1879 fax: (803) 736-8058

“Everyone knows that debugging is twice as hard as writing a program in the first place. So if you're as clever as you can be when you write it, how will you ever debug it?” BRIAN KERNIGHAN

From: Aaron Eischeid [mailto:notifications@github.com] Sent: Tuesday, November 25, 2014 11:50 AM To: tracefirst/usaha_committee Cc: Michael Martin Subject: Re: [usaha_committee] Species Code List (#42)

At GlobalVetLink we collect Species and SpeciesType, I wonder if some adoption of a similar distinction would be helpful for this document. I just feels really odd to have Beef, Bison, Bovine, and Dairy as 'species' maybe it should not be called species, but something without a distinct meaning like 'animalType' if these are the the codes that need to be accepted for whatever reason.

— Reply to this email directly or view it on GitHubhttps://github.com/tracefirst/usaha_committee/issues/42#issuecomment-64431405.

[aeischeid]

I agree that "For simple use cases like CVIs, two elements is probably the easier approach to implement" I would be in favor of Species + Production Class as you mentioned. To me that seems straight forward while being simple enough.

[mkm1879]

PGN Pigeon just bit me in the #$@@. We get a lot of CVIs for racing pigeons going out of state to start racing back. I've added it to my "relaxed" schema. This points to an issue with our terminology. Even though traceability doesn't really care about pigeons, traceability does care about getting the standard widely used. And users have to process even the weird species. Even though we provide "Other" that doesn't satisfy the use case where we really do need to communicate the weird species (in this case from Civet to USAHERDS using a list pulled from USAHERDS but going through the standard.)

[StaceySchwabenlander]

You'll have to forgive me, but I'm trying to understand how to read the [#42] Replaced SpeciesCodeType list with new values - the pink information is not the species list, it is the information in green that is the species list? Am I understanding this correctly? If so, this doesn't seem to match the information published on the USAHA site: http://www.usaha.org/Committees/AnimalHealthSurveillanceandInformation/AHSISDataStandards.aspx

The species list in that document seems to match the area in pink, not green. Can anyone clarify? Thanks!

[mkm1879]

I agree, it looks like the Word document on the USAHA site was made from an older copy of the draft. This raises the larger issue of keeping the standard current with the committee's work during the DSTU period. Should the "official" version be frozen until some date when all agreed upon updates are made? Or should we ballot interim point version upgrades?

[mkm1879]

One more weird species has reared its head here in SC. Much of our NPIP paperwork arrives with just POU-Poultry. That has been a valid "species" in USDA databases, etc. I'm "hacking" that into our local work. Do we want it in the standard when we do the next round? We have the even more generic AVI-Avian.

[mkm1879]

Me again. There is a huge potential list of minor species that can legitimately be included on CVIs. The ones that reared their heads here recently are all the game bird species. I think I've listed commercial pigeons earlier. (Not a minor species to our commercial producer here in SC.) I think we need to think about how we support those while avoiding an explosion of codes.