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2020-09-23 08:09:50

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2020-09-23 08:11:11

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Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-23 20:00:57

this might be useful https://theodi.org/article/data-ethics-canvas/

theodi.org
The Data Ethics Canvas – The ODI
Original URL: https://theodi.org/article/data-ethics-canvas/
👍 Åshild (Ash), Betsy Nelson, Pete Heintzman
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-24 07:44:01

and CARE: https://www.gida-global.org/care

image.png
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-24 11:25:05

another one: https://www.enrich-hub.org/bc-labels

👍 Anneke ter Schure, Åshild (Ash)
Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-24 11:44:11

I am attending a working group for Omics/eDNA + Ethics + Data and will ask for some of the slides that I believe will be very useful

👍 Betsy Nelson
Åshild (Ash) (ashild.v@gmail.com)
2020-09-24 11:59:05

*Thread Reply:* That would be great! Thanks @Antonio Fernandez-Guerra!

Antonio Fernandez-Guerra (antonio@metagenomics.eu)
2020-09-24 12:03:32
Omics_eDNA, Ethics & Data+Info Society.png
ivelsko (velsko@shh.mpg.de)
2020-11-03 19:47:55

Hi @channel! Now that we’ve had some time to process everything we covered in SPAAM2 and can look at it from a broader perspective, I think it would be great to start drafting this open letter to the aDNA field on raw data sharing. Is anyone keen to take up the reigns and spearhead the initiative?

Does anyone have ideas that they’d like to offer as a starting point or framework for the letter? Even putting forward thoughts that have just been floating around would be a nice way to get this rolling

👍 Kelly Blevins
Kelly Blevins (blevinske1@gmail.com)
2020-11-06 00:48:03

*Thread Reply:* I have been thinking about a section on sharing archaeological/paleopathological/bioarchaeological metadata. I would like to emphasize the importance of sharing skeleton/sample IDs as given by the curating institution and including photographic record of sampling location for pathological lesions.

ivelsko (velsko@shh.mpg.de)
2020-11-09 08:46:25

*Thread Reply:* That sounds great! Would you start a shared google doc with that information to get things rolling? You can pin a link to the doc in this channel for easy access

👍 Kelly Blevins
Kelly Blevins (blevinske1@gmail.com)
2020-11-10 19:45:17

Hi, @channel! I created a Google Drive directory to store our #datasharing thoughts, things, and outline. Feel free to add things and put your thoughts in the google doc.

Open letter on data sharing

💃:skin_tone_4: Miriam Bravo
ivelsko (velsko@shh.mpg.de)
2020-11-10 19:53:53

*Thread Reply:* Awesome, thanks!

💀 Kelly Blevins
Betsy Nelson (nelson@shh.mpg.de)
2020-11-10 22:37:40

*Thread Reply:* I currently have a manuscript draft that covers aspects of data sharing that might come up in the letter so I am going to wait a bit to access the Google Doc. Looking forward to joining in ASAP.

Nico Rascovan (nicorasco@gmail.com)
2021-09-23 19:31:27

Hello everyone

Nico Rascovan (nicorasco@gmail.com)
2021-09-23 19:34:24

I was wondering if any of you have already some good metagenomic datasets from the following sources:

  1. Modern oral microbiomes
  2. Ancient oral microbiomes with a very good and neat oral microbiome signature
  3. Soils and sediments (i.e., potential environmental contaminants in an ancient oral microbiome)
  4. Skin Microbiomes
Nico Rascovan (nicorasco@gmail.com)
2021-09-23 19:35:01

These are for @Camila Duitama who is running some source tracking analyses and needs the best possible standards for each of these 4 sources

Camila Duitama (camiladuitama@gmail.com)
2021-09-23 19:35:05

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Nico Rascovan (nicorasco@gmail.com)
2021-09-23 19:36:07

Maybe @James Fellows Yates, @irinavelsko, @Sterling Wright, etc.?

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-09-23 19:36:12

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Sterling Wright (sterlingwright2016@utexas.edu)
2021-09-23 19:36:12

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James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-09-23 20:36:18

Ooofff that's a hard one

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-09-23 20:36:25

You can try the ones i had in my paper

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-09-23 20:36:32

But they are all quite hard

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-09-23 20:39:13
  1. What do you mean by oral? Buccal? Saliva? Tongue?
  2. Check the Dir ;)
  3. Also a difficult one because so many modern soil samples involve treatments. But there are also sediment stuff of various contexts in the Dir. But saying what are potential contaminants or not is very hard to say. We don't know what does contaminate consistently, and it's probably context dependent
  4. In my PNAS paper I used some palm swab samples iirc
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-09-23 20:40:18

Well overall you could look at the PNAS paper, i used samples from all those categories in one way or another, but I can't guarantee they are 'good'. They are just what I could find 3 years ago and seem ed reasonable at the time (and took a LONG time to find)

Nico Rascovan (nicorasco@gmail.com)
2021-09-23 22:26:17

Answers:

  1. Whatever that will help you assess whether an ancient metagenome has a clear oral microbiome signature
  2. Camila has already downloaded most if not all ancient metagenomes of interest from the Dir. That was the first thing she did,…because the Dir is sooo good!
  3. Yes, sure, there is not universal contaminants. She is just using some soil datasets. I think adding some sediments from the Dir will be a good idea.
  4. Ok, great. I actually think I gave her those from your PNAS to download for this purpose… heheh
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-09-24 09:31:29
  1. you could either use plaque which sort of works, or actual modern calculus samples (there are the JAE samples in @irinavelsko’s paper in Microbiome, and the VLC ones in the PNAS one. I used modern plaque from HMP in my case.
  2. 👍
  3. I think that would be the ideal, as at least shallow sediments would more likely reflect burial environments (depending on the contex tof your samples), and also anicent ecologists do less wierd shit 😬 . Although on the otherhand a lot of the sampels IIRC (@Pete Heintzman might know) in the Dir' are like lake sediments which might not be the best
👍 Camila Duitama
Nico Rascovan (nicorasco@gmail.com)
2021-09-28 17:33:34

*Thread Reply:* What does IIRC stand for?

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-09-28 18:27:13

*Thread Reply:* If I remember correctly

Nico Rascovan (nicorasco@gmail.com)
2021-09-28 18:46:38

*Thread Reply:* eh?

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-09-28 19:59:23

*Thread Reply:* IIRC

If I Remember correctly

Nico Rascovan (nicorasco@gmail.com)
2021-09-28 21:17:39

*Thread Reply:* HAHAHAHA!

Nico Rascovan (nicorasco@gmail.com)
2021-09-28 21:17:55

*Thread Reply:* 😅😨

Nico Rascovan (nicorasco@gmail.com)
2021-09-28 21:19:26

*Thread Reply:* excuse my poor acronymglish

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2021-09-24 09:31:42

Ultimately: there is no easy answer or dataset. But it would be cool if someone made one 😉

Nico Rascovan (nicorasco@gmail.com)
2021-09-24 10:08:51

Awesome James! Thanks a lot, once again!

Camila Duitama (camiladuitama@gmail.com)
2021-09-25 09:47:16

Great! Thanks @James Fellows Yates

👍 James Fellows Yates
Sterling Wright (sterlingwright2016@utexas.edu)
2023-06-14 17:50:53

Could anyone share with me the HOPS database?

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-06-14 18:24:00

*Thread Reply:* What exactly do you mean by the HOPS 'database'?

Sterling Wright (sterlingwright2016@utexas.edu)
2023-06-14 18:47:49

*Thread Reply:* Sorry the one mentioned in this paper: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1903-0. At the end, it says "HOPS database is available upon request."

BioMed Central
HOPS: automated detection and authentication of pathogen DNA in archaeological remains - Genome Biology
High-throughput DNA sequencing enables large-scale metagenomic analyses of complex biological systems. Such analyses are not restricted to present-day samples and can also be applied to molecular data from archaeological remains. Investigations of ancient microbes can provide valuable information on past bacterial commensals and pathogens, but their molecular detection remains a challenge. Here, we present HOPS (Heuristic Operations for Pathogen Screening), an automated bacterial screening pipeline for ancient DNA sequences that provides detailed information on species identification and authenticity. HOPS is a versatile tool for high-throughput screening of DNA from archaeological material to identify candidates for genome-level analyses.
Original URL: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1903-0
James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-06-14 18:50:08

*Thread Reply:* Ah, you'll need to email Alexander Herbig for that

Sterling Wright (sterlingwright2016@utexas.edu)
2023-06-14 18:50:36

*Thread Reply:* Will do. Thanks.

James Fellows Yates (james_fellows_yates@eva.mpg.de)
2023-06-14 18:51:12

*Thread Reply:* Because there isn't actually a specific database for hops just the one they used for that paper (it's basically any malt database, they just used a specific set of genomes in that one)

👍 Sterling Wright
Ophélie Lebrasseur (ophelie.lebrasseur@liverpool.ac.uk)
2023-06-21 09:10:33

*Thread Reply:* Hello @Sterling Wright, My message may come too late, but in case this is still useful, I was asked to use that database as well, and my colleague and I found the following in the HOPS github: https://github.com/rhuebler/HOPS/blob/external/Resources/default_list.txt

<https://github.com/rhuebler/HOPS/blob/external/Resources/default_list.txt | default_list.txt>
<p>``` African swine fever virus Aspergillus fumigatus Bacillus anthracis Bacillus cereus group Bartonella bacilliformis Bartonella henselae Bartonella quintana BK virus strain AS BK virus strain GS BK virus variant RF Blastomyces dermatitidis Bordetella Bordetella pertussis Bordetella petrii Borreliaceae Borrelia Borreliella afzelii Borreliella burgdorferi Borreliella garinii Borrelia recurrentis Brucellaceae Brucella Brucella abortus Brucella melitensis Brucella microti Brucella ovis Brucella suis Burkholderia cepacia Burkholderia mallei Burkholderia pseudomallei Chlamydia abortus Chlamydia caviae Chlamydia felis Chlamydia muridarum Chlamydia pecorum Chlamydia pneumoniae Chlamydia psittaci Chlamydia trachomatis Clostridium Clostridium botulinum Clostridium botulinum BKT015925 Clostridium botulinum E3 str. Alaska E43 Clostridium sporogenes Clostridium tetani Clostridium tetani E88 Coccidioides immitis Coccidioides posadasii Corynebacterium diphtheriae Cowpox-Vaccinia virus Cowpox virus Coxiella burnetii Cryptococcus gattii species complex Cryptococcus neoformans Cynomolgus Epstein-Barr Virus A4 Cynomolgus Epstein-Barr Virus Si-IIA Cynomolgus Epstein-Barr Virus TsB-B6 Enterobius vermicularis Epstein-barr virus strain ag876 Epstein-barr virus strain p3hr-1 Escherichia coli Escherichia coli O111 Escherichia coli O157:H7 Escherichia coli O26 Fusobacterium Fusobacterium nucleatum Francisella tularensis Haemophilus influenzae Haemophilus influenzae Rd KW20 Helicobacter pylori Hepatitis B virus Recombinant Hepatitis C virus 3a-2a (SA1/JFH1) Hepatitis delta virus Hepatitis E virus Herpes simplex virus 1 strain R-15 Herpes simplex virus (type 1 / strain 17) Herpes simplex virus (type 1 / strain A44) Herpes simplex virus (type 1 / strain Angelotti) Herpes simplex virus (type 1 / strain CL101) Herpes simplex virus (type 1 / strain CVG-2) Herpes simplex virus (type 1 / strain F) Herpes simplex virus (type 1 / strain HFEM) Herpes simplex virus (type 1 / strain HZT) Herpes simplex virus (type 1 / strain MGH-10) Herpes simplex virus (type 1 / strain MP) Herpes simplex virus (type 1 / strain Patton) Herpes simplex virus (type 1 / strain R19) Herpes simplex virus (type 1 /strain RH2) Herpes simplex virus (type 1 / strain SC16) Herpes simplex virus unknown type Human herpesvirus 1 Human herpesvirus 6B Histoplasma capsulatum Human adenovirus 1 Human adenovirus 11 Human adenovirus 11+34 Human adenovirus 11a Human adenovirus 11p Human adenovirus 12 Human adenovirus 14 Human adenovirus 14a Human adenovirus 14p Human adenovirus 14p1 Human adenovirus 15 Human adenovirus 15/H9 Human adenovirus 16 Human adenovirus 16p Human adenovirus 17 Human adenovirus 18 Human adenovirus 19 Human adenovirus 19a Human adenovirus 19C Human adenovirus 19p Human adenovirus 1 strain Adenoid 71 Human adenovirus 2 Human adenovirus 20 Human adenovirus 21 Human adenovirus 21a Human adenovirus 22 Human adenovirus 22H8 Human adenovirus 23 Human adenovirus 24 Human adenovirus 25 Human adenovirus 26 Human adenovirus 27 Human adenovirus 28 Human adenovirus 29 Human adenovirus 30 Human adenovirus 31 Human adenovirus 3+11p Human adenovirus 32 Human adenovirus 33 Human adenovirus 34 Human adenovirus 34a Human adenovirus 35 Human adenovirus 35+11 Human adenovirus 36 Human adenovirus 3+7 Human adenovirus 38 Human adenovirus 38H44 Human adenovirus 39 Human adenovirus 3p Human adenovirus 40 Human adenovirus 41 Human adenovirus 41 Wisconsin Human adenovirus 42 Human adenovirus 43 Human adenovirus 44 Human adenovirus 45 Human adenovirus 46 Human adenovirus 47 Human adenovirus 48 Human adenovirus 49 Human adenovirus 4a Human adenovirus 5 Human adenovirus 50 Human adenovirus 50 prototype strain Wan Human adenovirus 51 Human adenovirus 52 Human adenovirus 53 Human adenovirus 54 Human adenovirus 55 Human adenovirus 56 Human adenovirus 57 Human adenovirus 58 Human adenovirus 59 MSJ-2011 Human adenovirus 6 Human adenovirus 60a Human adenovirus 61 Human adenovirus 62 Human adenovirus 63 Human adenovirus 64 Human adenovirus 65 Human adenovirus 66 Human adenovirus 67 Human adenovirus 68 Human adenovirus 69 Human adenovirus 7 Human adenovirus 71 Human adenovirus 7428 Human adenovirus 7620 Human adenovirus 7961 Human adenovirus 7a Human adenovirus 7d Human adenovirus 7d2 Human adenovirus 7h Human adenovirus 7l Human adenovirus 7m Human adenovirus 7p Human adenovirus 8E Human adenovirus 9042 Human adenovirus 9052 Human adenovirus 9431 Human adenovirus A02-2B-2 Human adenovirus A03-2B-1 Human adenovirus AdV/Berlin Human adenovirus AdV/Berlin003/02/DE Human adenovirus AdV/Berlin004/02/DE Human adenovirus AdV/Berlin131/01/DE Human adenovirus AdV/Berlin524/01/DE Human adenovirus AdV/Berlin604/01/DE Human adenovirus AdV/Berlin619/01/DE Human adenovirus AdV/Berlin643/01/DE Human adenovirus AdV/Berlin682/01/DE Human adenovirus AdV/Berlin718/01/DE Human adenovirus AdV/Berlin749/01/DE Human adenovirus AdV/Berlin769/01/DE Human adenovirus AdV/Berlin859/01/DE Human adenovirus ATCC VR-1501 Human adenovirus ATCC VR-1502 Human adenovirus B1 Human adenovirus B2 Human adenovirus B3 Human adenovirus Chiba_E086/2012 Human adenovirus D10 Human adenovirus D13 Human adenovirus D15H9 Human adenovirus D17H29 Human adenovirus D19H30 Human adenovirus D30H44 Human adenovirus D37 Human adenovirus D37H13 Human adenovirus D37H17 Human adenovirus D46H13 Human adenovirus D8 Human adenovirus D9 Human adenovirus E4 Human adenovirus H02-2B-2 Human adenovirus H02-2B-3 Human adenovirus H03-2B-1 Human adenovirus H08-2B-2 Human adenovirus I02-2B-2 Human adenovirus I05-2B-2 Human adenovirus isolate MY7/1 Human adenovirus isolate MY8/1 Human adenovirus isolate SGH2289 Human adenovirus isolate SGH5253 Human adenovirus LZY153B Human adenovirus MKJ/Chennai/2010 Human adenovirus RKI-2797/04 Human adenovirus S02-2B-1 Human adenovirus S03-2B-1 Human adenovirus S03-2B-2 Human adenovirus S03-2B-3 Human adenovirus S05-2B-2 Human adenovirus S06-2B-3 Human adenovirus S07-2B-2 Human adenovirus S08-2B-3 Human adenovirus S10-1-6 Human adenovirus type 35p Human hepatitis A virus Human herpesvirus 3 strain Dumas Human herpesvirus 3 VZV-32 Human herpesvirus 3 strain Oka vaccine Human gammaherpesvirus 4 Human mastadenovirus C JC polyomavirus JC virus x BK virus Klebsiella oxytoca Klebsiella pneumoniae Klebsiella pneumoniae subsp. rhinoscleromatis Legionella pneumophila Leptospira alexanderi Leptospira alstonii Leptospira borgpetersenii Leptospira broomii Leptospira fainei Leptospira inadai Leptospira interrogans Leptospira kirschneri Leptospira kmetyi Leptospira licerasiae Leptospira noguchii Leptospira santarosai Leptospira weilii Leptospira wolffii Methanobrevibacter oralis Moraxella catarrhalis Mycobacteroides abscessus Mycobacterium africanum Mycobacterium avium Mycobacterium bovis Mycobacterium canettii Mycobacterium colombiense Mycobacterium intracellulare Mycobacterium kansasii Mycobacterium leprae Mycobacterium tuberculosis complex Mycoplasma pneumoniae Neisseria Neisseria gonorrhoeae Neisseria meningitidis Orthohepadnavirus Parvimonas micra Peptostreptococcus anaerobius Plasmodium falciparum Plasmodium vivax Pneumocystis carinii Pneumocystis jirovecii Porphyromonas gingivalis Porphyromonas gingivalis W83 Rickettsia africae Rickettsia akari Rickettsia conorii Rickettsia felis Rickettsia japonica Rickettsia prowazekii Rickettsia rickettsii Rickettsia sibirica Rickettsia typhi Salmonella enterica subsp. enterica Salmonella typhimurium TR7095 Schistosoma mansoni Shigella boydii Shigella dysenteriae Shigella flexneri Shigella sonnei Simian virus 42 Staphylococcus aureus Streptococcus Streptococcus agalactiae Streptococcus anginosus Streptococcus dysgalactiae Streptococcus gordonii Streptococcus gordonii str. Challis substr. CH1 Streptococcus mutans Streptococcus oralis Streptococcus pneumoniae Streptococcus pneumoniae Streptococcus pyogenes Streptococcus salivarius Streptococcus sanguinis Taenia solium Tannerella forsythia Tannerella forsythia 92A2 Toxoplasma gondii Trepone…</p>
<a href="https://github.com/rhuebler/HOPS">rhuebler/HOPS</a>
Sterling Wright (sterlingwright2016@utexas.edu)
2023-06-22 00:21:24

*Thread Reply:* Thank you!