Perl 6 - the future is here, just unevenly distributed

IRC log for #opentreeoflife, 2014-03-26

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01:06 towodo jimallman, ok, I was sort of wondering about that. I hate being tied to a particular version of anything but if we need to be, so it goes.
01:07 jimallman i think it's a necessary evil, since I'm patching several web2py files that change over time (oauth2_account.py, etc)
01:08 jimallman we've been lucky so far. if we want to do something more robust (maintain a patched fork of web2py, and try to keep it in sync?), i'm game to discuss it.
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18:52 kcranstn towodo: implications of modifying silva as per laura's email?
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19:06 travis-ci [travis-ci] OpenTreeOfLife/api.opentreeoflife.org#443 (local-dep - 6b24f0e : Emily Jane McTavish): The build passed.
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19:12 towodo kcranst, laura continues to show that she doesn't understand silva.
19:13 towodo There are no 'curated tips' in the SILVA tree marked as Genus species strain.
19:13 towodo The tips in the tree are accessions (about 500,000 of them).
19:14 towodo In the SILVA user interface, you see many accessions marked Genus species strain, but the label is just retrieved from NCBI, it is not 'curated' and it is not in the SILVA tree.
19:15 towodo She says:  "Uncultured bacterium GB#AB630682" and "Uncultured bacterium GB#FR667489” (which are in two different clades)
19:15 towodo those are not clades, those are sequences.
19:16 towodo s/kcranst/kcranstn/
19:16 kcranstn she says that they are IN two different clades, not that they ARE two different clades
19:16 towodo Her message is wrong in so many ways I don't know where to start...
19:17 kcranstn all of the SILVA tips are accession numbers
19:17 towodo unless she somehow knows a lot more biology than I do, and I am just completely clueless.
19:17 towodo Actually they aren't even accession numbers, they are particular 16s sequences.
19:18 towodo They are in no sense "curated". They are retrieved automatically by mining genbank.
19:18 towodo SOmetimes several tips come from the same genbank accession.
19:25 towodo I think she is sure she understands SILVA and won't listen to me if I try to explain how it works.
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19:35 towodo kcranstn, Unless she means to pick just one genbank accession# at random to add to the taxon name? I.e. if SILVA taxon Genus has accesions a, b, c, d, and of those four two of them say a, c are labeled by NCBI as 'Uncultured bacterium", then pick either a or c, and tack it on to 'Uncultured bacterium' to get a string to display in the browser?
19:40 kcranstn let me push forward with getting the strain names from genbank and see how far that gets us
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19:44 towodo it will make things better in the case that the ncbi taxon is Genus species, but it won't help in any of the uncultured cases that she's talking about.
19:44 kcranstn what if we did include them as uncultured bacterium Z93545 and link to the accession?
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19:49 kcranstn I know that it is inconsistent with how names work in the rest of the tree...
19:49 kcranstn and I don't like the fact that we are unlikely to map future phylogeny tips to these tips
20:00 towodo A SILVA clade (genus level - there are no species-level clades in SILVA) could easily contain 500 accessions, all labeled by NCBI as 'Uncultured bacterium'. Do we have 500 OTT tips in this case?
20:00 towodo (there are no strain-level clades in SILVA either by the way)
20:00 kcranstn is part of the problem that the downloads don't match the UI?
20:01 towodo not sure what you mean
20:02 kcranstn so things in the UI like "Actinobaculum urinale DSM 15805" are exclusively tips and not clades?
20:02 towodo they are neither. I think that's what's confusing.
20:03 towodo they are groupings of accessions based on having been given the same taxon name label
20:04 towodo this was the approach Jessica took when she wrote the SILVA script, and it seemed good to me, since it allows us to align SILVA with NCBI
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20:05 towodo and of course by aligning with NCBI, we get to match SILVA accessions with accessions that aren't in SILVA (that might be OTUs in source trees)
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20:09 kcranstn "having been given" -> by whom?
20:09 kcranstn manually or automatically?
20:09 towodo by ncbi curators or depositors.
20:09 kcranstn ok
20:10 kcranstn and I see that string shows up in the UI but not in the fasta file
20:11 towodo there should be an ncbi taxon xref, or something like that. the silva script for OTT finds the taxon id. then each id has a name string associated with it
20:11 towodo in the ncbi taxonomy record for that id
20:13 towodo on the web page http://www.ncbi.nlm.nih.gov/nuccore/FR667489 you will see /db_xref="taxon:77133"
20:13 kcranstn yup
20:13 kcranstn got that
20:14 towodo when the web page is composed they retrieve the taxon name for that id and put it on the ORGANISM line
20:18 kcranstn I see that many of the accessions are from ENA not genbank?
20:18 kcranstn is there overlap between the two resources?
20:19 towodo I'm not completely sure, but I'm pretty sure that each caches the other. You can look up any accession number in either.
20:19 kcranstn ok
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