Organism Classification

Organism Classification: Conservation Status

2008-08-26T21:57:06.0012Z

IUCN Red List http://www.iucnredlist.org/search/search-basic

This site has a lots of useful info.

Organism Classification: Splitting existing Wikipedia articles on combined subspecies

2008-06-23T20:11:59.0012Z

That was an internal link. Try http://www.freebase.com/view/guid/9202a8c04000641f800000000544e143#namespaces instead.

Organism Classification: Splitting existing Wikipedia articles on combined subspecies

2008-06-21T00:23:35.0012Z

The updated link is dead too.

Python family: Don't merge

2008-06-18T23:50:11.0012Z

This topic is for the family of pythons; the other topic is for the genus.

Organism Classification: Hmmm

2008-06-12T06:19:11.0005Z

This is going to be more difficult than I thought. Then again, it should be a good way of learning more about data modelling. Thanks for the feedback!

Tomato: tomato and tobacco

2008-06-12T01:59:22.0000Z

Check out the Toxic compounds in potatoes section of the Potato Wikipedia page.

Light to potatoes is like food after midnight to gremlins. Keep 'em in the dark if you know what's good for you.

Tomato: tomato and tobacco

2008-06-12T01:23:23.0000Z

Interesting. I didn't know that either. What's more, potato is also in the same family.

Tomato: tomato and tobacco

2008-06-12T01:03:26.0005Z

I was really surprised at the nightshade connection. If i remember correctly sir Walter Raleigh broung tobbaco from the New World to Jolly Old England. but I bet no one ever smoked tomato's?

Organism Classification: Conservation Status

2008-06-11T20:37:42.0001Z

I happened to be looking at my state's endangered & threatened wildlife list and they had both state and federal status.

So that might be something to consider. Even if you only want to do federal level, it should be clear that it is.

And something else I just thought of, is you'd probably need a country field, or source/location, so people knew where it was endangered/threatened.

Organism Classification: Conservation Status

2008-06-11T20:01:33.0000Z

I agree with Ed's suggestion about the model, but I would add a date for delisting as well.

What I'd recommend is creating an "organism classification" type (or something similarly-named) in your private domain with the "conservation status" property, and try out some models there. Post back here (or on the data-modelers' list) when/if you want feedback. If it seems to work well, it could eventually get moved to the commons Biology domain.

Organism Classification: Conservation Status

2008-06-11T05:41:15.0007Z

I'd suggest modeling an "organism conservation status" type or something more inclusive sounding and then add it on a case by case basis. For example, I have imported Partners in Flight conservation status codes that are only applicable to birds in the Western Hemisphere. These should probably be added as part of CVTs with date and location properties. You could also add US conservation categories of threatened and endangered or subset it for state listings.

I would create a CVT with status code (that links to the status classification system), date, and location at a minimum. For example, Bald Eagles are going through a US federal delisting period but may still be listed as endangered at the state level in some states and their status today in the US is different than it was a year ago. So, those three properties (code, date, location) should be sufficient but are also essential.

Organism Classification: Conservation Status

2008-06-11T04:28:19.0005Z

I'd like to add a "conservation status" property to the schema, so that I can start adding endangered/extinct species data.

I'm assuming that "organism classification" would be the right topic...

Organism Classification: Filling in ITIS Taxon S/N manually?

2008-05-26T04:01:55.0000Z

Seems to be working now - thanks!

Ovenbird: Merge with the other Ovenbird

2008-04-22T01:23:41.0007Z

The permission for ITIS is currently set to "Global Write Permission" -- which is probably not ideal. It should be set to the same one NCBI has:

http://www.freebase.com/tools/explore/guid/9202a8c04000641f8000000003cc0361

Sadly I don't think changing this will fix what's going on here though...

Ovenbird: Merge with the other Ovenbird

2008-04-21T23:16:44.0007Z

OK, the "enumeration" type is correct, but the inability to edit the property is definitely not. I've reported the problem to the ones one reports such problems to.

Ovenbird: Merge with the other Ovenbird

2008-04-21T22:15:31.0029Z

Bizarre. The properties for ITIS and NCBI have an expected type of the system type "enumeration" instead of "machine readable string" or something more normal for foreign keys. This is almost certainly an error -- I'll try to find out what's going on here.

Ovenbird: Merge with the other Ovenbird

2008-04-21T21:47:56.0000Z

Oops.

Shouldn't there be an ITIS and NCBI for the species? I tried adding the ITIS TSN for this species (726205) and Freebase would not store it.

Ovenbird: Merge with the other Ovenbird

2008-04-21T21:12:51.0007Z

Don't merge -- one is for the family of ovenbirds, and one is for a species with the common name "ovenbird".

Magnoliopsida: Merge Dicotyledon and Magnoliopsida

2008-04-14T03:58:38.0000Z

I notice that Wikipedia has separate entries for the two ... It does seem that they should be merged, but there might be a broader issue about which classification system to use. Is ITIS a non-controversial reference?

Ovenbird: Merge with the other Ovenbird

2008-04-13T17:52:11.0012Z

There are two topic pages for the organism classification of Ovenbird.

Organism Classification: Filling in ITIS Taxon S/N manually?

2008-04-02T05:37:33.0007Z

Thanks, much appreciated.

Organism Classification: Filling in ITIS Taxon S/N manually?

2008-04-02T02:41:10.0007Z

Thanks, Luke; I’ve reproduced it and filed a bug report on this issue.

Organism Classification: Filling in ITIS Taxon S/N manually?

2008-04-02T00:41:01.0005Z

I recently created the Pentalagus classification (for a genus which just contains one species, so didn't have a Wikipedia stub).

If I click on the "Edit" button next to "ITIS Taxon S/N", the usual dialog box opens, requesting me to enter an enumeration. I can enter 625308 (the serial number according to www.itis.gov); however, the "save" button stays grey. If I click on it anyway, the circles flash indicating that data is being saved; however, when this completes, the value that I entered is not there.

I'm using Firefox v2.0.0.11 if that helps.

Organism Classification: Filling in ITIS Taxon S/N manually?

2008-03-31T19:09:49.0014Z

What kind of trouble, Luke? An Enumeration is just a special kind of machine-readable string; you should just be able to enter the value as for any other property. Or are you not sure what value to enter?

Organism Classification: Filling in ITIS Taxon S/N manually?

2008-03-30T23:28:26.0012Z

I'm having trouble filling in the ITIS Taxon S/N (an Enumeration) manually ... is there any particular procedure I should follow to do this?

Organism Classification: Reconciling Wikipedia, Topics and ITIS

2008-02-24T07:53:06.0000Z

Great job! I'm looking forward to using it.

Organism Classification: Reconciling Wikipedia, Topics and ITIS

2008-02-24T04:56:10.0012Z

I have reconciled some data from ITIS which now annotates almost 39k organism classifications. The Mass Data Operation is described here . While the import was very conservative, im sure their may be errors. Please let me know of any that you find and Ill address them for the next import.

Organism Classification: Splitting existing Wikipedia articles on combined subspecies

2008-01-26T00:14:58.0007Z

This thread seems to have died off, but I wanted to correct JG's link about namespaces for any new users going through and reading up on what's happened in the past. The URL has changed slightly, you can now find the info here.

Organism Classification: Moving Person attributes to Organism

2007-10-11T20:19:54.0007Z

By the way, the upshot of this discussion was that there are properties of Dog like "Dog Owner" which we may want to alias with properties from Person like "Pets owned". This relies on an uncoming aliasing feature, so we're waiting on that.

Human: Need at least one version of the article for the subspecies

2007-09-30T22:15:14.0012Z

If we do split this article, one version needs to be the version that is properly an Organism Classification for Homo sapiens sapiens as the biological subspecies.

Organism Classification: Breed as a rank

2007-09-28T19:51:47.0000Z

I support doing simple modeling for now, having a link to the standards for each organization.

Horse breeding is as complicated as dogs, if not more so. Cats as well. I think there a few more critters with breeding standards similar to the dog breed type. Camels? ;)

Organism Classification: Breed as a rank

2007-09-28T06:35:48.0007Z

For the breed standards, we've been looking at Labrator Retriever which seems to be a relatively simple case. For a more complicated case, see the Wikipedia infobox for Poodle. It's not obvious that all of the breed groups are the same, such as "Group 9 Section 2 #172" and "Group 7 (Non-Sporting)". Also, some kennel clubs have multiple links to standards, such as ANKC. Again, it seems to me that the question is whether Freebase really needs to capture all of this in a compound value type, or whether a simple link to each of the kennel clubs is enough. What do you think?

Organism Classification: Breed as a rank

2007-09-24T07:22:26.0007Z

By that, do you mean that the currently-named Purebred Dog type should just be "Dog" and we should add any other dog properties besides Breed such as, maybe, Owner? Or are you talking about changing the Dog Breed type used on topics like Labrador Retriever?

Organism Classification: Breed as a rank

2007-09-24T06:10:33.0007Z

I suspect that Dog breed is a very Dog specfic thing, and that it should be modeled on a Dog type for now.

Organism Classification: Moving Person attributes to Organism

2007-09-22T01:10:34.0012Z

For anyone watching this discussion, you may want to look at the thread on the Data-modeling email list called "Should some of the Person attributes be moved to Organism?"

(Followups should go on the email list.)

Organism Classification: Breed as a rank

2007-09-21T01:06:13.0007Z

... in other words, this is really an issue of citation. For example, Thomas Jefferson has religion Deism. But says who? One biographer may say this, but another will claim he was Christian. This can only be resolved by settling on a best guess and citing sources. Likewise, the American Kennel Club says a Labrador Retriever has "height at the withers 22½ to 24½ inches", but the New Zealand Kennel Club says otherwise. The only point I can see of citing 7 different kennel clubs is to burden the user with opening all those pages and researching the disagreements over the definition of a Labrador Retriever.

Organism Classification: Breed as a rank

2007-09-21T00:55:23.0000Z

Both these points beg this question: The American Kennel Club defines specific properties of a Labrador Retriever such as "The height at the withers for a dog is 22½ to 24½ inches". If these are important enough to link to, shouldn't this information be pulled into Freebase as its own topic such as "AKC Standard: Labrador Retriever"? Then the link to the AKC web site would just be a normal "Web LInk" link on the topic as an external reference. Conversely, if the details of the different definitions of the American Kennel Club, the Canadian Kennel Club, etc. don't matter enough to pull into Freebase, then why complicate the Dog Breed type with properties to link out to these?

Organism Classification: Breed as a rank

2007-09-21T00:16:05.0007Z

Re dog breed groups, if different clubs have different groups with the same name, we should have different topics for them (like different kinds of fictional humans).

Organism Classification: Breed as a rank

2007-09-20T21:01:49.0007Z

I am a firm believer in the DogCow! Long may Clarus live!

I am unaware of any major differences in group specifications...I guess none of the three of us are that well-versed in dog breeding groupings and classifications for breeds (I've watched some of the dog shows on TV because of the wife's interest in big-head dogs, and Best of Show movie, of course). I concur with the notion of the simplest CVT possible for now.

My wife I will ask tonight for more insight into this arcane world of doggery. She's expressed an interest in the past in being able to research for specific traits of a breed (temperment, activity level, size, weight, etc. Here is a bit simplistic site for what would be good data to have for each breed: Canine General Characteristics )

Ex. Akita

Intelligence
Stubborn
Strong Prey-Drive
Protective
Rarely Barks
Weight-Range
Heavy Fur Shedding

Organism Classification: Breed as a rank

2007-09-20T18:17:02.0007Z

OK, I changed it to a single CVT. See Labrador Retriever. But if as you say, "the dog breed group enum list will be the same for all clubs" then this argues that it should not be in the breed standard CVT for each club, but should be outside, such as the "country of origin" property. Or is there a case where two clubs specify different dog breed groups?

Organism Classification: Breed as a rank

2007-09-20T17:06:27.0007Z

Don't you mean "woof", Gordon?

Jeff: this is indeed a bonny start. I would recommend going with a generic CVT for the club standards, however, for two reasons. First is that, either way, the "dog breed group" enum list will be the same for all clubs (the list is identical in your two sample CVTs because the properties in each point to the same type). In order to have different enum lists for each club, we'd actually need separate types for each club's dog breed groups, which I think would be unnecessarily complex. The other reason is just that I think it's less complicated to have a single CVT that has properties for club, group, and website.

Organism Classification: Splitting existing Wikipedia articles on combined subspecies

2007-09-12T03:03:59.0007Z

Neato! I hadn't heard about this proposal.

Organism Classification: Splitting existing Wikipedia articles on combined subspecies

2007-09-08T07:49:50.0007Z

we are prototyping a mechanism like that based on http://www.ietf.org/internet-drafts/draft-gregorio-uritemplate-01.txt

Organism Classification: Comparison of richness/detail of candidate data sources

2007-08-29T21:25:21.0007Z

You are right that the higher classification jumps to the Superfamily. This is merely because there were no imported articles from Wikipedia for the intermediate ranks. In some cases, I did create stub topics to fill in the rank. For example, Homo Sapiens. I'm curious to see how John's data load algorithm will fill in intermediate topics from ITIS, etc. I'd say that if one of these authorities defines an intermediate rank such as Infraclass that we should use it.

Organism Classification: Comparison of richness/detail of candidate data sources

2007-08-29T01:43:40.0000Z

On the 'Higher Classification': I noticed that the higher classification of the Ganges and Indus River Dolphin was River dolphin, i.e. going from a Species to a Superfamily. It seems that this is the only member of its Genus and Family - would we want to create an entry for each regardless?

Might there be cases where the Infraclass is not commonly used and some authorities would jump straight to Class? (Not that this is relevant, but I'd never heard of Infraclass before finding it on Freebase ... :)

Organism Classification: Splitting existing Wikipedia articles on combined subspecies

2007-08-28T16:33:04.0007Z

I see. I thought you were talking about a Freebase mechanism to automatically convert the ID into a link so that you could click on /biology/itis/180547 and it would open the page on ITIS. Is there a mechanism like that for the UI?

Organism Classification: Comparison of richness/detail of candidate data sources

2007-08-27T22:36:57.0000Z

Looks good. I asked Jamie to promote your type to /biology.

Organism Classification: Comparison of richness/detail of candidate data sources

2007-08-27T06:39:37.0007Z

I added Synonym Scientific Name and made Scientific Name a unique value. See Sea Otter. (I though just 'Synonym' would be confused with 'Also known as'.)

BTW, I also set 'Higher Classification' to unique value. Is there a good argument for allowing multiple values?

Organism Classification: Splitting existing Wikipedia articles on combined subspecies

2007-08-27T06:00:36.0000Z

Namespaces are described here. Rather than loading ITIS ids as rawstrings, I could make them keys. The issue is where to create the namespace. For example /biology/itis/180547 could get you to http://www.freebase.com/view/%239202a8c04000641f80000000002b6696

Organism Classification: Comparison of richness/detail of candidate data sources

2007-08-27T05:54:38.0007Z

I think we need an additional text field for Synonym. Synonym is an 'alternative' scientific name, e.g. Mustela lutris rather than Enhydra lutris. We could put multiple scientific names but then we have to distinguish which are 'accepted'.

Common names should collide with the Topic name, Im hoping.