Biology

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.

Biology: "Found in" property?

2008-08-01T21:38:08.0012Z

Ooh, birds. You may want to talk to spatialed, from what I understand he's quite the expert on bird conservation. He's the creator of the Birds domain.

Biology: "Found in" property?

2008-08-01T01:45:34.0012Z

I agree, this would be great. Would it be worth adding a separate type(s)? For birds, something like "Migrating Bird" with Locations for where it spends summers and winters ... Maybe it's worth having a separate "Plant" type anyway, to capture perennial vs annual as well as native status ...

Biology: "Found in" property?

2008-07-31T16:50:07.0017Z

I'm interested in gardening (the landscaping kind) and a couple of the big issues/topics is using "native" plants and not using "invasives". I know in the US the states keep lists of what plants are considered invasive, or potentially invasive. Native is a whole can of worms (no agreement on what is really native), but we could at least use the plants.usda.gov info to show where the plants were found to be growing. It would present the data in a better way for analysis.

Related to this are animals in a given area. It would be great to be able to find what snakes, for example, live in a certain state or country. Or where else you can find your favorite bird, including see where it winters. I know there are databases out there that track at least the birds, but not sure if we can incorporate that somehow?

I'm not sure how any of this could fit in exactly, but I wanted to mention it in case anyone had any ideas.

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.

Biology: Proposed Taxo import

2008-04-01T01:09:46.0019Z

This question is probably better discussed on the developers mailing list.

However, the reason that spreadsheets are supported first is that it is easy for non-technical people with domain expertise to understand a spreadsheet, and a mapping is fairly straightforward.

Freebase data is not hierarchical; it is a general graph, which can represent hierarchies, but isn’t constrained the way XML is. That means that the mappings are more complex, and probably better handled with a custom application, at least until we come up with some superduper UI assistant.

If the data you want to import can be flattened, then a flat import tool can be used, but otherwise, you will probably need some kind of application that comprehends and maps your data.

Biology: Proposed Taxo import

2008-03-31T23:47:29.0000Z

> This brings us to the topic of datasets. There are several efforts in the world at a comprehensive database of life. The ones I have studied (in no particular order) include:

> ITIS
> Species 2000
> DiscoverLife
> NCBI
> EOL
> International Plant Names Index
> Wikispecies
> Wikipedia-en taxoboxes

There's Tree of life which I've mentioned before but which apparently has a licensing issue.

http://www.tolweb.org/tree/home.pages/downloadtree.html
( http://www.dbfordummies.com/Example/Ex710.asp )
( http://paste.uni.cc/11838 )

For butterflies and moths there is BAMONA and All Leps.

(Bamona isn't easily accessible online however the maintainer Thomas Naberhaus is willing to create an extract for use elsewhere; I'm working with him on that just now in fact for a Flickr project to create a leps field guide)

http://www.lepbarcoding.org/files/nth_am_lep_full_checklist.xls

I have a question which may be more appropriate in some techie thread but I'll ask it here anyway since the specific example that first brought it to mind was the TOL dump; will there be facilities for importing via XML? It seems at least as useful as spreadsheet imports.

Spreadsheets seem fine for flat data typical of a relational database, but I hope that Freebase has support for hierarchical data as well.

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?

Prion: Detyped as a "disease or medical condition"

2008-03-12T21:34:31.0000Z

Yay! Thanks Jeff. I see you have already reciprocated the property from "Disease or medical condition" -- perfect!

What types are you referring to when you said classifications can be done with additional types?

Prion: Detyped as a "disease or medical condition"

2008-03-12T20:36:27.0007Z

Well, since you asked so nicely :), go on over to disease cause and play around. You can handle the classifications by adding additional types to the topics.

Prion: Detyped as a "disease or medical condition"

2008-03-12T08:23:56.0061Z

A prion causes diseases, but is not one. I've detyped it.

We need additional properties! I'd like to be able to enter causes of diseases, and their classification (virus, infection, prion, parasite, etc.).

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 Rank: Hybrids?

2007-12-15T02:26:55.0005Z

Where does hybrid fit in this type? Should it be typed as its own rank?

Protein: Working on urls

2007-11-15T08:17:20.0007Z

yes definitely. we need some protein schema design help. any experts out there?

Protein: Other Properties?

2007-11-15T01:09:03.0005Z

I am not a biochemist, but wouldn't it be useful to add more properties to proteins? e.g. Protein Family (http://en.wikipedia.org/wiki/Protein_family) and/or which organism(s) they are commonly found in?

Biology: Selecting species from a certain kingdom

2007-10-25T10:26:16.0000Z

Sounds like a good plan of action jg :-) Looking forward to updates.

Biology: Selecting species from a certain kingdom

2007-10-25T07:41:47.0007Z

Well it turns out that they are not distinguished in ITIS. http://www.itis.gov/vernac.pdf

I propose that if the first name matches the Wikipedia name we leave it alone, and we load all the vernaculars as /common/topic/alias. For new topics from ITIS we use the first name, capitalize the first word and use the remainder (if any) as aliases.

Biology: Selecting species from a certain kingdom

2007-10-25T04:49:13.0000Z

OK, let me look at the actual ITIS database and see if we can distinguish one as primary, which would allow the others to be aliases....

Biology: Selecting species from a certain kingdom

2007-10-23T09:31:08.0000Z

Here's a better example http://www.itis.gov/servlet/SingleRpt/SingleRpt?search_topic=TSN&search_value=34342 has 5 common names listed.

Biology: Selecting species from a certain kingdom

2007-10-23T06:34:30.0007Z

For that specific example, Spring Crocus may be too generic. For example this database only has the other common name http://plants.usda.gov/java/profile?symbol=CRVE4

Biology: Selecting species from a certain kingdom

2007-10-23T06:01:32.0007Z

>>> Sure. For example Crocus vernus ( http://sandbox.freebase.com/view/crocus_vernus ) has two common names, Dutch Crocus and Spring Crocus. If I have followed correctly the final format would be that one of the two common names would be the Name, 'Crocus vernus' is in the Scientific Name field and the remaining common name can be added as an alias? <<<

That sounds right.

>>> Thanks for the prompt replies guys. <<<

Now that they've got the RSS feeds working, the discussion boards work a lot better.

Biology: Selecting species from a certain kingdom

2007-10-22T20:43:21.0000Z

>>> Can you give an example? Usually the common name (if known) is the topic title and the scientific name is in the Scientific Name field. <<<

Sure. For example Crocus vernus ( http://sandbox.freebase.com/view/crocus_vernus ) has two common names, Dutch Crocus and Spring Crocus. If I have followed correctly the final format would be that one of the two common names would be the Name, 'Crocus vernus' is in the Scientific Name field and the remaining common name can be added as an alias?

>>> As for common names, I agree with Jeff that they should be the name field, and there is alias if we need it. Also ITIS has many names in Spanish, which I plan to import. <<<

Above all I was curious as to how common names would be handled because I didn't see a common name field per say. It never occurred to me that the Name field may be used :)

Thanks for the prompt reply guys.

Thanks for the prompt replies guys.

Biology: Selecting species from a certain kingdom

2007-10-22T19:08:51.0007Z

Frank, we dont expect the query to be slow, but as soon as we have the data loaded Ill try it out. Some databases (e.g. Species 2000 have a field which is the flattened complete hierarchy, which we could fall back to if we need it)

As for common names, I agree with Jeff that they should be the name field, and there is alias if we need it. Also ITIS has many names in Spanish, which I plan to import.

Biology: Selecting species from a certain kingdom

2007-10-22T17:56:37.0007Z

Can you give an example? Usually the common name (if known) is the topic title and the scientific name is in the Scientific Name field.

Biology: Selecting species from a certain kingdom

2007-10-22T14:58:58.0000Z

Also sorry for the double post but will the 'Also known as' field contain a plant's common names from the ITIS data? I'm working on a web application to incorporate this data and because users search a lot by common name it would be very useful to have. Double thanks!

Deceased Organism: Possible aliasing with Deceased Person

2007-10-12T04:43:56.0007Z

Also, on the data-modeling list, I think a good argument was made for not including "Cause of Death" right now for animals:
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