Hello, and thank you for listening to the MicroBibCade podcast. Here, we will be
discussing topics in microbial bioinformatics. We hope that we can give you some
insights, tips, and tricks along the way. There is so much information we all
know from working in the field, but nobody really writes it down. There's no
manual, and it's assumed you'll pick it up. We hope to fill in a few of these
gaps. My co-hosts are Dr. Nabil Ali Khan and Professor Andrew Page. Nabil is the
Head of Informatics at the Quadram Institute in Norwich, UK, and Andrew is the
Director of Technical Innovation for Liagen in Cambridge, UK. I am Dr. Lee Katz,
and I am a Senior Bioinformatician at Centers for Disease Control and Prevention
in Atlanta, United States. Welcome back. We're here at day three of GMI, where
Page is slowly taking over everything, which is great. Being in Page and all
that. So, I'm here with Lee again, and Ruth. So, Ruth, do you want to introduce
yourself? Sure. I'm Ruth Timme. I'm with the U.S. Food and Drug Administration,
and I run the Genome Tracker Program, FDA's Genomic Epidemiology Program for
foodborne pathogens. Awesome. So, you're the guys who deposit, like, hundreds of
thousands of salmonella in the public domain? Hundreds of thousands is probably
an overestimate, but we deposit a lot. Yeah, more than a lot. Yeah, at one
point, I think I was the biggest submitter of Listeria, and then I was quickly
overtaken by Ruth on submitter of pathogens for NCBI. So, what do you actually
do day-to-day? That's a hard question. Well, so, FDA funds a couple dozen
laboratories to sequence data, and so there's a lot of back and forth with
working with them, making sure the data is submitted in a standardized way, and
if it's not, you need to update it. So, there's a lot of work like that. And
then I also work a lot of interagency stuff with the U.S., CDC, USDA. And then
on the international side, I work with PAGE to try to make sure that standards
we're putting in place are kind of adopted internationally. And you've just been
working on the DOM. What is the DOM? So, the pathogen data object model is this
idea that whole genome sequence data for any kind of pathogen should be
submitted and stored in the same structured format in the INSDC. And you would
think this is a very simple idea, but you would be surprised at how many
different ways you can submit the pathogen genome to the INSDC and store
metadata in all different locations. So, it's very confusing for submitters and
people querying to figure out where that information is. But is this yet another
standard, or is it like a standard to rule them all? Well, it would just be one
standard within INSDC. Once you set it there, then the third-party apps can just
plug into it. You don't have to understand that. You don't have to worry about
it, that your Salmonella standard is going to be different from a virus
standard. It's all the same. That's really cool, actually. Long overdue.
Although, yeah, we should have had that years ago. But it is doing some good
work. So, what was before the DOM model? We were submitting stuff before that.
How does it make things better? How are we doing it before DOM model? So, I
thought that this had already been said, because we had said it for foodborne
pathogens a decade ago, and we all plugged into it. We have third-party
applications plugged into it. Makes submission very easy. Makes retrieval very
easy. I thought that's how the world worked. And then when I started seeing the
COVID genomes come in as biosample records only, and people were merging
metadata onto the flat file, and then building pipelines to do that and query
it. It's like, oh, no. Then I realized, actually, in the virus world, that's not
a standard. Yeah, I mean, viruses do everything differently, don't they? Even
naming conventions and everything are totally crazy. So, if you query viruses in
the INSDC, I don't know, 50% of them don't contain a biosample. Wow. Actually,
yesterday, I was accused of not uploading data when I had to INSDC, but it's
actually because it's so complicated when you deal with, say, multi-country,
multi-institution organizations, and these standards don't necessarily reflect
everything. You know, one lab gives it to another lab, gives it to another lab,
gives it to us to sequence, and we upload, and then it's a huge, big, roundabout
way of doing everything. You got a gotcha question yesterday about that. Yeah,
yeah, and I did look, and actually, it was all in there. We had actually
submitted our COVID raw data with metadata. With a biosample? With a biosample,
of course. Oh, absolutely. And with the consensus genomes as well. You know, a
lot of people don't do that, but for some reason, it's not showing up as it
should. You know what, genome, I think it still doesn't have a biosample. Am I
wrong about this? Is Wuhan one? Doesn't have a biosample. Yeah, it's just a
GenBank record. I think it's frustrating that when the first one comes in like
that, it's really easy just to, you know, copy that. Yeah, anyway, hopefully for
the next pandemic, we will learn some lessons. One thing I wanted to get into,
just really quick, is Andrew, you keep saying, like, so everything is phage
here. What are we doing at GMI? And I thought maybe Ruth had a good answer to
that. Like, where is the divide? I'm not sure. I think my emerging thoughts are
GMI is a good place to discuss the standards that are being set in other
organizations. GMI has a strong intergovernmental presence here. Had good
collaborations with WHO, FAO, and ministries of health in other countries. And,
you know, one role, and I'm not sure what the future of GMI is, right? But one
role could be that we look at standards set by groups like phage and then figure
out how to implement them in the real world. Yeah. Which I think is a much
harder part than just creating the standards. Yeah, I feel like what I'm seeing,
I'm agreeing with you. What I'm feeling is phage has a lot of hands on the
technical stuff that nobody's wanted to pay attention to before the virus rolled
just now. And that GMI is the political part of this whole thing, where they
have context, how to implement it, how to get uptake from different governments.
I think that's a really good distinction. Maybe. Maybe GMI can just be like a
subgroup of phage, where, you know, it's the political subgroup. I've thought
about that. I'm not sure how that would work. It'd be a disaster, wouldn't it?
No comment from government people here. But it is actually quite nice that
there's so much overlap between the two groups. And, you know, you've got phage,
which is actually getting stuff done and producing papers, producing, you know,
actual functional code, producing specifications, you know, things that are
useful to the world. And then GMI, obviously, is bringing people together to
discuss those. And, you know, it's a presentation platform. Awesome. Well, thank
you very much, Ruth, for talking to us. And I'm sure we will catch up to you
again. Thanks for having me. Thanks. Thank you so much for listening to us at
home. If you like this podcast, please subscribe and rate us on iTunes, Spotify,
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And if you don't like this podcast, please don't do anything. This podcast was
recorded by the Microbial Bioinformatics Group. The opinions expressed here are
our own and do not necessarily reflect the views of CDC or the Quadram
Institute.