Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2015-02-02

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All times shown according to UTC.

Time Nick Message
00:08 kcranstn joined #opentreeoflife
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15:42 kcranstn mtholder - are you there?
16:06 kcranstn pinging mtholder
16:07 mtholder I have to leave in 2 minutes to catch my bus...
16:07 kcranstn ok, let me know when you get back post-transit
16:08 mtholder ok
16:08 kcranstn (trying to label branches and nodes on that figure for discussion tomorrow)
16:16 jar286 I can’t believe we’re getting more snow…
16:16 kcranstn we are getting more rain here
16:16 jar286 I mean, that we *have* more snow. looks like about a foot since last night
16:17 kcranstn wheeee
16:17 jar286 that wouldn’t be a problem except that there’s no place to put it
16:57 mtholder joined #opentreeoflife
17:14 jar286 kcranst, u there?
17:14 jar286 kcranstn, u there?
17:14 kcranstn here
17:14 jar286 i think i have to go back to working on dryad
17:14 jar286 fyi
17:15 kcranstn yeah, that’s been ignored for a while
17:16 jar286 really want to work on synthesis, but it’s great that mtholder is on the hunt, he might take care of it
17:16 jar286 I meet with Peter tomorrow
17:16 kcranstn ok
17:16 kcranstn about stats?
17:17 jar286 well, about both things, stats and taxonomy
17:17 jar286 did you see the milestone I created?  April 17, for microbes… wanted your thoughts
17:18 jar286 we can talk tomorrow
17:18 kcranstn yes, lets talk tomorrow
17:18 kcranstn (haven’t looked at the milestone yet - been occupied with synthesis)
17:45 mtholder joined #opentreeoflife
17:45 mtholder kcransn, I'm back (with beer, even)
17:46 kcranstn trying to label nodes and edges on that figure from SAS
17:46 kcranstn let me send you what I have so far
17:47 mtholder there is a cleaner example (without D), but we don't have a pretty graph for it.
17:48 kcranstn https://www.dropbox.com/s/fxbm49sb4ubr3o3/example_tm.pdf?dl=0
17:49 mtholder the nodes are right.
17:49 kcranstn step 1…
17:49 mtholder step 1 adds D, and node 11 and E
17:49 kcranstn yup
17:49 mtholder D and 11 because they are from tree 1
17:50 mtholder E because it does not overlap with the "relationship taxa" of either
17:51 mtholder did you want me to continue, or did you want me to just confirm that the node #s are correct.
17:51 mtholder ?
17:52 kcranstn and edge labels?
17:52 mtholder thats more tedious.
17:52 kcranstn If my node and edge labels are correct, then I understand what’s going on
17:52 mtholder I can get them if you need them.
17:52 mtholder one sec. I can confirm some from the logs...
17:53 kcranstn I don’t *need* them, but if folks want to discuss the example tomorrow, it might be easier if we had labels on nodes and edges
17:54 kcranstn although “green branch between 10 and 13” is probably enough
17:54 kcranstn so let’s leave it with nodes
17:54 mtholder let me fire up my version of neo4j.
17:54 kcranstn nah, its dine
17:54 kcranstn fine
17:54 mtholder its not a big deal.
17:56 mtholder ok it is running. one more sec...
17:57 mtholder r17 is correct
17:58 mtholder taxo edge from D is r16
17:58 kcranstn I think I can leave that off because it is not controversial
17:58 mtholder agreed.
17:58 mtholder there are actually lots of edges suppressed in that graph.
17:59 mtholder it is now easy for me to check, so let me know if there is another one that you want me to check.
18:01 mtholder oops. r16 an (irrelevant) MRCA from E->root. r15 (with the ? in the figure) is the uninteresting edge to D.
18:01 mtholder from D.
18:02 kcranstn ah, I might add that one because stephen mentions it in the issue
18:04 kcranstn can you check 23, 45 adn 33?
18:04 mtholder 23 is from A to 10
18:04 mtholder r45 is from 13 to 10
18:05 mtholder r33 is also correct in the figure.
18:05 kcranstn cool, thanks
18:05 mtholder looks good.
18:05 kcranstn is this thereofore incorrect:
18:05 kcranstn “Another oddity is that when node 13 (the mrca of A, B, and E which one would like to see in the final tree) is rejected as a dauther of node 10, it appears that node 13 is rejected because synthesis has just moments earlier added A as a child of node 11:
18:05 kcranstn should be ‘added A as a child of node 10’?
18:06 kcranstn https://github.com/OpenTreeOfLife/treemachine/issues/157
18:06 mtholder you're right child of 10
18:08 mtholder fixed on the issue.
18:09 kcranstn ok, updated figure in agenda for tomorrow
18:09 mtholder thamks
18:09 mtholder s/m/n/
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22:37 jar286 jimallman, I wonder if the ‘node properties’ should show the submitted-by person, not the last curator (e.g. Bacteria shows me! because I added a DOI)
22:37 jar286 ?
22:38 jimallman we actually store a list of all contributing curators in nexson.. i wonder if oti is only capturing the last one.
22:38 jar286 probably.
22:38 jimallman (i noticed this with the tags and submitted an issue. should we do the same here?)
22:38 jar286 so the ‘submitter’ is the first one?
22:39 jimallman i would think so, yes. i append the curator’s name to the end of the ot:curatedBy list, if they’re not already listed.
22:39 jar286 yes I think there should be an issue. I can do it.  Against OTI, right?… the browser just shows what it gets
22:39 jar286 not sure how it works
22:39 jimallman on second thought, this data is probably coming from treemachine and not oti.
22:39 jar286 right…
22:40 jimallman part of the response to https://devapi.opentreeoflife.org/treemachine/v1/getSyntheticTree
22:40 jar286 is it out of the question for the browser to get this information from oti or some other source?
22:40 * jimallman is taking a closer look at the JSON now, to make sure i’m using all the submitter data
22:40 jar286 stephen really doesn’t like putting the responsibility on treemachine
22:40 jar286 and it’s sort of the wrong modularity
22:41 jar286 curator knows about submitter.
22:41 jar286 but that’s from the nexson I guess
22:42 jimallman this data is coming from the ‘sourceToMetaMap’ property of the JSON from getSyntheticTree
22:44 jimallman i’ve checked all the sourceToMetaMap entries in the JSON for ‘cellular organisms’, and all entries have just one curator name listed
22:44 jar286 right, that’s what I thought
22:47 jimallman here’s where the metadata is added: https://github.com/OpenTreeOfLife/treemachine/blob/0087bfbdc012aa7982391929fd769f8e6000f72d/src/main/java/org/neo4j/server/rest/repr/ArgusonRepresentationConverter.java#L151-L156
22:48 jar286 just wondering about the cost of getting this info from some other place, like OTI
22:49 jar286 (maybe with a new service)
22:49 jar286 it could be fetched lazily, when you click on node/edge
22:49 jimallman ah, i see what you mean.
22:50 jimallman would this potentially handle your long-standing desire for “tell me more about this taxon/node”?
22:51 jar286 no, that’s in a different place - in OTU mapping
22:51 jar286 but same idea, yes
22:51 jimallman gotcha. in any case, we do have the study ID in argus, so I could get slightly smarter data from oti
22:52 jar286 not high priority
22:52 jar286 maybe I will file an issue on the opentree repo
22:54 jimallman i just confirmed that oti keeps just one curator name (mine) in this study:  https://devtree.opentreeoflife.org/curator/study/view/2845
22:55 jimallman it should show both me and Joseph (who i believe was the original submitter)
22:55 jar286 yep
22:56 jimallman i’m adding this to my existing oti issue: https://github.com/OpenTreeOfLife/oti/issues/35
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