Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2015-03-23

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All times shown according to UTC.

Time Nick Message
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14:21 jar286 jimallman, there?
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15:08 jimallman jar286: here now
15:08 jar286 hi
15:09 jimallman i see the wiki page has changed since i was there last, just got caught up.
15:09 jar286 did you look at http://wiki.datadryad.org/Open_Tree_/_Dryad_handshake ?
15:09 jar286 oh sorry
15:09 jar286 crossed messages
15:09 jimallman yes, that’s the page i’m reading
15:10 jar286 I think there are just two main things left to do, the open tree UI and the ‘claim’ logic in Dryad
15:10 jar286 hangout?
15:10 jimallman gotcha. i’m hazy in the notion of a “claim check”, but most of the rest makes sense to me.
15:11 jar286 (I’ve invited to you google chat so that I can easily create the hangout)
15:11 jimallman hangout is good. i need a minute, will ping you
15:11 jar286 ok
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15:46 josephwb colleague just came back from Paleobiology Database hackathon.
15:46 josephwb because they know we, they were asked repeatedly:
15:46 josephwb What is the stance of the OTOL project with regarding integrating data on extinct/fossil species?
15:47 josephwb i don't know how to answer, other than (we tried early on, taxonomies were terrible, so we focused on extant taxa"
15:48 josephwb thoughts kcranstn, jar286?
15:48 kcranstn not opposed to it, but need high-quality taxonomies that contain fossil data (alternately, a better UI for adding taxa from trees when taxa aren’t in OTT)
15:48 josephwb i feel the extant taxonomy is getting a fairly decent vetting, but extinct taxonomy unseen?
15:49 josephwb unseen == not looked at/corrected
15:49 jar286 hang on…
15:52 josephwb wish i knew tha PBDB hackathon was going on; one of us could have gone
15:56 jar286 jimallman, our connection just failed…
15:56 jar286 I think we’re done though
15:56 jar286 so thanks for the help
15:56 jimallman likewise!
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16:48 josephwb jar286 what is the diff between extinct_direct and extinct_inherited
16:48 josephwb ott references taxomachine source, but no info there: https://github.com/OpenTreeOfLife/taxomachine/blob/master/src/main/java/org/opentree/taxonomy/OTTFlag.java
16:51 josephwb kcranstn : do you know? ^
16:51 kcranstn I would assume that direct are marked as extinct and inherited and taxa descdended from an extinct_direct taxa, but I don’t know for sure
16:52 kcranstn “and inherited are taxa"
16:52 josephwb inherited extinction seems weird
16:56 kcranstn having an extinct taxa with non-extinct descendents also seems weird
16:58 josephwb yeah
16:58 josephwb i guess extinct_inherited means "extinct, and parent taxon is extinct, too"
16:59 kcranstn I suspect “extinct, because parent taxon is extinct”
16:59 josephwb oh...
17:00 kcranstn as opposed to extinct_direct = “some other source said this was extinct”
17:00 kcranstn (I am channeling the thought process of jar286, so I might be wrong)
17:01 josephwb is that a useful dichotomy? it is certainly confusing the paleo people looking at it.
17:02 kcranstn direct is a data point, and inherited is inferred
17:03 kcranstn answering the question “why does OTT think this is extinct?"
17:03 josephwb i suspect the derived taxa have data points too
17:03 josephwb i can check if any have both direct and inherited
17:03 kcranstn yes, that is true
17:03 kcranstn there are taxa with both
17:04 kcranstn and taxa with only one of the two statuses
17:11 josephwb so: just extinct.
17:12 kcranstn ?
17:12 josephwb i mean, both mean: "extinct"
17:12 kcranstn yes, both mean extinct. differ in the “why"
17:12 josephwb right
17:12 josephwb btw, there are *no* docs on this
17:13 josephwb these definitions must have undergone some scrutinizing
17:15 kcranstn probably not as much as you might hope
17:15 kcranstn https://github.com/OpenTreeOfLife/reference-taxonomy/wiki/taxon-flags
17:15 josephwb yeah, links to taxomachine code, but no info there
17:16 josephwb where would i put an issue: OTT or taxomachine?
17:16 josephwb the former, probably
17:16 kcranstn https://github.com/OpenTreeOfLife/reference-taxonomy/issues
17:17 josephwb making one now
17:20 josephwb done
17:23 jar286 josephwb, extinct_direct means that the taxon is directly annotated as being extinct
17:23 jar286 extinct_inherited means it is reachable tipward from such a taxon
17:24 jar286 e.g. if a genus is extinct_direct, then any species in it must be extinct (ergo, extinct_inherited)
17:27 jar286 the documentation is here https://github.com/OpenTreeOfLife/taxomachine/blob/master/src/main/java/org/opentree/taxonomy/OTTFlag.java
17:28 jar286 the direct/indirect business is described for other flags, but not that one
17:28 kcranstn notes distinction between ‘documentation’ and ‘code comments'
17:29 jar286 no inherent difference, you’re talking about discoverability
17:30 kcranstn and user friendliness
17:34 jar286 you mean formatting?
17:34 kcranstn comments in code rarely give the sort of overview that I would expect from documentation
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