Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-01-28

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Time Nick Message
02:14 jimallman joined #opentreeoflife
05:15 frankbutt joined #opentreeoflife
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13:46 blackrim joined #opentreeoflife
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15:10 blackrim anyone play with scrollback? lowers the barrier of entry to chatting on irc. i added a listener. you can play here http://scrollback.io/opentreeoflife/
15:13 kcranstn ok, went there. Now what do I do?
15:13 sb-heitut joined #opentreeoflife
15:13 sb-heitut testing
15:14 blackrim1 joined #opentreeoflife
15:14 blackrim1 well, you can chat just like you do in IRC
15:14 blackrim1 this is embeddable which is cool
15:15 blackrim1 of course, you can also login so that you get a recognizable name (when I type in scrollback, it shows up as blackrim1 in irc because the name is taken)
15:16 sb-heitut1 testing while logged in as me
15:17 kcranstn ok, how do I switch to my account from this sb thing?
15:17 kcranstn (I am logged in on scrollback)
15:17 blackrim haha, it just changed the name slightly on IRC but I see it right on scrollback. I am sure it would be right if you closed and reopened scrollbck
15:17 blackrim I didn't do that but I logged in before opening the opentreeoflife one
15:17 sb-heitut1 testing again
15:17 kcranstn damn
15:18 blackrim no need to curse
15:18 blackrim sb-dation?
15:18 sb-heitut2 ok, logged out and back in again
15:18 sb-heitut2 yay!
15:18 blackrim I am also going to logout and see what happens
15:18 sb-iturts I am now logged out
15:19 blackrim2 I am logged back in
15:19 blackrim I closed the window. I wonder how long it keeps that sb-binsto there
15:20 blackrim Anyway, just thought that could be a nice addition if folks wanted to also come over but didn't want to go into irc. I think it just stays active until I turn it off
15:20 blackrim got the idea from Hilmar over at #phyloirc
15:26 towodo joined #opentreeoflife
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15:49 blackrim joined #opentreeoflife
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16:06 blackrim by the way, that jarble user that you see there is from scrollback. Just messing around with other ways of joining the IRC without coming on. if you go to http://scrollback.io/opentreeoflife/ you will see what I mean. Otherwise, ignore
16:20 jimallman joined #opentreeoflife
16:36 blackrim towodo: can the tattered bits be dealt with with the taxonomy edit file? the individual corrections? or are they too complex for that? thinking of the ones that are synonyms
16:36 towodo they can certainly be handled by patching.  the problem is that there are 4000 of them
16:37 towodo and 73 used as OTUs...
16:37 towodo not sure how many in synthesis, probably a handful
16:41 blackrim yeah, seems like we just have to start somewhere. joseph mentioned that he would be happy to do the birds.
16:41 blackrim we definitely don't need to do them all for publication or anything
16:42 josephwb is draft 13 the one to fix, or is there a newer one?
16:43 blackrim draft 15 was just uploaded
16:43 blackrim presumably the problems are still there though.
16:44 blackrim seems like some of the empirical folks have had some issues with the patch file. Wondering if there is a way that we can get them doing it without getting confused or messing things up
16:51 kcranstn1 joined #opentreeoflife
16:51 kcranstn1 do you know what the issues are?
16:51 blackrim they are unique for each one. sometimes synonyms, sometimes misspellings, etc
16:51 josephwb some rank problems too
16:52 blackrim yeah
16:52 kcranstn so the issues are data, not that they are having problems editing the files at github
16:52 blackrim oh, i misunderstood the question
16:52 kcranstn np
16:52 josephwb the rank problems shouldn't hinder things, unless they get excluded because of rank conflicts
16:52 blackrim the problems with editing the files.
16:53 kcranstn1 left #opentreeoflife
16:53 kcranstn more detail, please
16:53 blackrim you are talking about the editing of the patch file? right? not the actual problem with the taxonomy bit
16:53 kcranstn (I wrote that documentation, so if I can update it to help, happy to do so)
16:53 kcranstn yes
16:55 blackrim here is the info for the patch https://github.com/OpenTreeOfLife/opentree/wiki/Interim-taxonomy-patch-feature
16:56 blackrim I think that, at least Bryan, had some issues getting things into the right format
16:56 blackrim of course, remember that many of these folks are not well versed in what is plain text files, plain text editors, etc. So while it is pretty simple, I think there just have been some issues with getting them right.
16:56 blackrim josephwb: haven't you done some patching?
16:57 josephwb nope
16:57 blackrim josephwb: you just sent things direct to jonathan
16:57 josephwb but jonathan recently gave me some example code
16:57 josephwb yup
16:58 josephwb documentation looks pretty god to me
16:58 blackrim yeah, i think the doc is fine.
17:02 josephwb some of the links are dead, though: https://github.com/OpenTreeOfLife/reference-taxonomy/tree/master/edits and https://github.com/OpenTreeOfLife/reference-taxonomy/blob/master/edits/ott_edits.txt
17:02 kcranstn are they editing on github, or doing local edits?
17:02 kcranstn thanks, josephwb
17:02 josephwb arg. didn't format correctly
17:02 kcranstn got them
17:02 josephwb "list of patch files", and "ott_edits.txt"
17:03 blackrim i can't imagine they are cloning (most don't know what github is) so they are doing local edits (that is what the instructions assume).
17:03 kcranstn local = on github
17:04 blackrim :-p sorry, i mean they are doing it on github itself, not local cloning
17:05 kcranstn ok, fixed broken links. towodo - let me know (or change the docs?) when the directory structure changes?
17:06 towodo i thought i changed the docs.
17:06 towodo in the wiki
17:07 kcranstn links were in two places in the docs
17:07 towodo oops.
17:07 towodo i have to go over them all by hand anyhow
17:08 towodo hmm.  feed/ott/edist/*.tsv in the old patch system. I have no convention for the new patch system
17:08 kcranstn towodo: them = docs, or them = patch files?
17:08 towodo the patch files.
17:09 kcranstn because people aren't following the instructions?
17:09 towodo all the ones i've received have been full of errors, badly formatted etc.
17:09 towodo fundamentally it's because there's no feedback
17:09 kcranstn can you give me some examples, and I can communicate back to folks?
17:10 towodo the instructions can say that the files have to have tabs, but they have no way to tell whether they do or not
17:10 towodo you have to give parent taxon names, but often the parent is ambiguous. there'd be no way for them to know
17:10 towodo (homonyms)
17:11 towodo the problem may have already been fixed by an ncbi update.  then the patches are innocuous but unnecessary
17:11 kcranstn "interim patch feature"
17:12 towodo right.   the "new patch feature" at least fixes the tabs problem, but comes with its own set of problems (probably)
17:13 towodo my 'they' sentence was garbled. did you get what i was saying? the curator has no way in the github editor to tell a tab from a non-tab
17:13 towodo if every row has the same number of columns (i.e. no # comments) things are better I think, then it's tabular editing
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19:25 kcranstn not sure if this is for blackrim or someone else, but the links under 'view taxonomy' and 'view simple synthetic tree' on http://files.opentreeoflife.org/ lead to mostly blank pages
19:26 blackrim I am guessing that could be because of the change in servers. I will check on that. Getting the new taxonomy processed so it can be loaded over there for everyone to take a look. Once that is there, I can check on the links unless towodo wants to
19:26 kcranstn have an EOL hackathon next week and will want to use both the taxonomy and synthetic tree
19:26 kcranstn and would like to share links with others on my team
19:30 blackrim sounds good. i will do my best.
19:30 kcranstn thanks!
19:31 towodo me too
19:34 towodo blackrim, the 'official' version of those links is in the web app at About > Developer resources, so in github
19:34 towodo .../opentree/webapp/views/about/developer_resources.html
19:34 kcranstn I am about to edit that page to replace the relative urls with pointers to files.opentreeoflife
19:34 towodo the files can stay on files.opentreeoflife.org
19:34 towodo ok
19:34 towodo where is your EOL hackathon? DC?
19:34 kcranstn nescent
19:35 kcranstn convenient
19:35 kcranstn :)
19:35 towodo i'll say
19:35 kcranstn gordon is going to be there, too
19:35 blackrim towodo: thanks for the note. so are you doing those edits (you said you were going to replace the relatives)
19:35 kcranstn I am
19:36 blackrim towodo: btw, the taxonomy tar is done and uploading is going on now to ot9 -- assuming that is still where we are putting things
19:36 towodo yes, put them there
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19:43 blackrim towodo: wondering why I am getting a GITHUB_CLIENT_ID not specified when I am pushing -- using this command push.sh -c ot9.config push-db treemachine.db.tgz treemachine
19:44 towodo changes Jim made last night. I thought I had communicated the need for github-free servers to Jim & Duke, but I guess not.
19:45 towodo their bug, not yours.  but if you want to adjust look at the documentation (opentree/deploy/sample.config)
19:45 towodo would you like me to report this?
19:46 towodo I don't think he's on line now
19:46 towodo jimallman, you there/
19:46 blackrim i can just add one
19:47 jimallman blackrim, towodo: apologies, i'm here
19:47 jimallman i can relax the error message for missing variables, make it a warning without exiting.
19:47 blackrim jimallman: no problem, I just put some dummy ones
19:48 jimallman ok, i'll make the change regardless. i wasn't thinking about scenarios where someone's simply not intending to use these components.
19:48 towodo yep.  or if the api is not one of the components, just don't say anything at all
19:49 towodo i can easily imagine a setup with opentree+curator on server A, api+oti on server B, and tree+taxo on server C
19:49 blackrim regardless, new taxonomy is moving over. give it an hour and then it should be up and I will let folks know -- with emphasis on understanding fossils should be gone
19:49 towodo some fossils will remain, because IRMNG is not comprehensive. but I think it should be the bulk of them
19:52 blackrim right
19:53 josephwb i think i may have missed something. are fossils taken out of the taxonomy now?
19:54 blackrim they don't have to be. they are identified with IRNMG. I am skipping them right now to see what is cleared up that has been problematic before. gbif has such bad placement for them that I think it is good to see it without them
19:54 blackrim we will obviously need to not do that for everything (e.g., dinosaurs)
19:54 josephwb okay
19:55 blackrim but I think almost all the plant fossils are junk and there are tons in fungi (?) that are junk
19:56 josephwb just want to note i have 1) a great dinosaur tree and 2) am waiting on a comprehensive primate tree that has all of the fossil taxa. i imagine these are the two clades people would look at for fossil.
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19:57 blackrim josephwb: aweseom
19:57 blackrim aweseom = awesome
19:57 kcranstn +1
19:57 kcranstn for the info and the funny
20:05 towodo Peter tells me that IF has fossil information. I haven't asked him to make this a priority yet, maybe it's time (or too late). We should see what David H thinks I guess
20:09 blackrim yeah, hopefully people will get back soon. i am thinking we are getting to the end of this?
20:13 josephwb just tested the dinosaur tree for mapping. a number (~half) are coming out from "Reptilia", which is a paraphyletic group, and so shouldn't be in the taxonomy.
20:14 josephwb seems that *every* child taxon of "Reptilia" has major flags
20:14 josephwb all are "tattered"
20:15 josephwb many rank conflicts
20:15 PEM <towodo> yes, happy to jump on the fossil taxa in IF if now's the time.
20:16 PEM <josephwb> based my experience with the phenoscape taxonomy, I'm not surprised dinosaurs are messy.
20:16 towodo if it's not too hard… if you just add a 'flags' column and put 'extinct' there for extinct taxa then it'll get merged
20:16 josephwb i think we will end up needing to get rid of Reptilia completely
20:17 PEM <towodo> got it.
20:17 towodo did you know Ornithischia is in NCBI?
20:19 towodo which as you know is all about sequences
20:19 mtholder there is a collagen sequence
20:20 josephwb http://www.ncbi.nlm.nih.gov/protein/P86290.1
20:20 mtholder http://www.ncbi.nlm.nih.gov/pubmed/19407199
20:21 mtholder mass spec -- now that is an expensive way to sequence.
20:21 blackrim towodo: just saw your email. should i go ahead and start working on 16 and just load when it is ready? i won't quit this one
20:21 blackrim is that going to mess with anything other than fungi?
20:23 josephwb 65220F58-A880-41B1-A50D-A29465018D5F-4615-00001B3E5AB8A4DF
20:23 josephwb tried to paste in an image. guess it doesn't work
20:23 towodo the problem fixed by draft16 is mainly about fungi but it potentially affects other things - not sure. basically it was causing information from the 'id source' (the previous version, 2.3) to pollute the new version, so e.g. what should have been hidden became unhidden
20:23 towodo it's really up to you. i didn't expect to fix it so quickly (assuming i did)
20:24 towodo sorry to be disruptive. i thought it might be better to batch the fix with other changes?
20:31 towodo blackrim, anyhow, draft16 is there for the taking if you want it
20:32 blackrim towodo: i will go ahead with it. it takes long enough for them to move and load that there will likely be some time for people to see
20:33 blackrim towodo: no matter to me
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20:51 kcranstn I was thinking about officially archiving the wikispaces site. Thoughts? We only have one active page - the nexson page. Could we move that to a github wiki?
20:51 blackrim towodo: quick question -- I uploaded treemachine.tgz but I see it saying Extracting database from downloads/treemachine.db.tgz. is it hardcoded to treemachine.tgz
20:52 kcranstn mtholder and PEM - the wikispaces archival would mostly affect the two of you
20:52 towodo it's hardcoded on the server side. on your machine you can call it whatever you like
20:53 blackrim ok, just making sure that we were all good
20:53 blackrim it is extracting and we should be live any second
20:53 kcranstn hey sckott - good to see you here!
20:53 sckott Hey, you too!
20:53 sckott Wasn't sure it this was active, looks like it
20:56 mtholder kcranstn: I won't scream loud enough for you to hear me if you do that. But I'm not anxious to translate wiki syntax or fix the links pointing to the NexSON page.
20:56 mtholder we also have pointed to it in email threads. so more link rot that we can't fix if it goes away.
20:57 blackrim ok, new taxonomy (15) is up at http://ec2-54-203-194-13.us-west-2.compute.amazonaws.com emailing folks now
20:58 kcranstn I can just change the main page to more accurately reflect how we are using the site and where other active documentation lies
20:58 towodo I say move the nexson page to github or a github wiki, and leave a forwarding address behind
20:58 towodo i can use emacs keyboard macros to rewrite markup if it comes to that
20:59 kcranstn there are mediawiki -> markdown converters
21:00 mtholder We have been using that wiki as the more mature docs, and the github wiki for less mature (which is not to say sophomoric, immature) suggestions. We can keep that convention and have 2 github pages. I just don't think we should dump it all in one. I'm fine with getting rid of it, if we can redirect that URL
21:02 towodo two pages with different purposes is of course fine
21:09 PEM <kcranstn> the wiki address is also in the in the nexson files currently.  Forwarding would work - I can also change the definition of link in the header if we decide on something more permanent.
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21:21 towodo ouch… the link in the nexson files themselves needs to be a purl
21:21 kcranstn agreed
21:23 towodo blackrim, taxonomy is looking better.  There's a 'reptilia' class, an example of 'tattered'.  Embarrassment?
21:23 kcranstn probably
21:27 towodo oh no. Bilateria incertae sedis
21:28 kcranstn towodo - what's your purl username?
21:28 towodo jar287
21:29 towodo need to give the password to the yougest person on the project :)
21:29 towodo s/youg/young/
21:29 kcranstn h
21:29 kcranstn a
21:30 towodo kcranstn, we should think about getting our own purl 'domain' so we don't have to use /NET/
21:30 kcranstn I just created purl.org/opentree/nexson -> http://opentree.wikispaces.com/NexSON
21:31 towodo oh wow, we do have our own domain! when did you do that?
21:31 kcranstn when I needed to give a purl to our data sharing page to nsf
21:31 kcranstn you are admin ;)
21:31 kcranstn I will create an issue on the phylesystem repo
21:45 blackrim towodo: sorry for the delay there. yeah i think reptilia will need to be corrected, but we will get there. that one is pretty bad
21:45 towodo There's a Pongidae, too, quite independent of great apes, and it's empty
21:47 towodo There are 17 'incertae sedis' containers leaking through. I see why & have fixed
21:48 blackrim how did pongidae make it through
21:50 towodo don't know. It's in GBIF but not NCBI. contains 3 genera all extinct (but one not marked extinct)
21:50 blackrim things are way easier to browse. i am assuming it is the extinct stuff gone
21:51 blackrim everytime I browse in plants, I find the image that is there to look like some sort of cephalopod
21:52 blackrim http://ec2-54-203-194-13.us-west-2.compute.amazonaws.com/opentree/otol.draft.22@2722891/eudicotyledons
21:52 blackrim image up close http://phylopic.org/image/30049b3c-eb09-4459-a34e-1963e13e2711/
21:52 kcranstn plants with legs!
21:53 blackrim yeah, i can see what it is going for up close but it gets me everytime :-p
21:55 towodo goodness, the spider families are one long flat list. ugh
21:56 blackrim haven't looked there
21:58 blackrim getting out of here
21:58 blackrim left #opentreeoflife
22:14 PEM <towodo> spiders (at least the RTA-clade) looks about as NCBI has it - not seeing a flat list.
22:29 towodo I'm looking at http://ec2-54-203-194-13.us-west-2.compute.amazonaws.com/opentree/otol.draft.22@995253/Arthropoda
22:30 towodo under 'Arachnida' we see a huge long list.  It's not spiders, sorry, it's arachnids
22:30 towodo maybe these are mostly fossils?
22:34 towodo PEM, picked one at random, and it turned out to be a mite… so the tree is wrong  http://eol.org/pages/3208412/overview
22:34 towodo the order info got lost somewhere along the way from ITIS to CoL to GBIF
22:37 PEM Mites are arachnids as well.  Spiders are Araneae.
22:41 towodo Yes, but that family should have been placed in Acari. Instead it's incertae sedis.
22:42 PEM That's a problem
22:43 towodo I suspect something like this is happening for most of those random Arachnida families. GBIF doesn't put them in orders. IRMNG does but for some reason the orders aren't being inserted into the taxonomy (paraphyly prevention probably)
22:43 towodo Looks like a significant GBIF snafu.
22:44 towodo Weird since ITIS has these things in orders and ITIS -> CoL -> GBIF
22:55 PEM left #opentreeoflife

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