In the very beginning of our Listeria project, we basically had an idea that we could use evolution to help in epidemiological investigations. The idea was out there in the world, and so I can't claim credit, but no one yet had the resources to sequence all Listeria monocytogenes genomes in a given area before HHS backed the project. I would love to write more about this project actually but I digress.
The point here is that we had a vocabulary problem. In the beginning in the CDC lab (I can't say what all was happening in the other agencies), we had some of the best epidemiologists and some of the best Listeria microbiology experts in the room, and also one bioinformatician (me). Thus, three different disciplines, one important project, and one huge vocabulary problem. I tried collecting all the terms that everyone had to learn in the room but that started turning into epi/micro/bioinformatics notes and became too huge.
Instead, I present here a list of confounding vocabulary terms that we all came into the room thinking we knew but instead had different meanings for different people. I also present my own suggested disambiguation for these terms.
The point here is that we had a vocabulary problem. In the beginning in the CDC lab (I can't say what all was happening in the other agencies), we had some of the best epidemiologists and some of the best Listeria microbiology experts in the room, and also one bioinformatician (me). Thus, three different disciplines, one important project, and one huge vocabulary problem. I tried collecting all the terms that everyone had to learn in the room but that started turning into epi/micro/bioinformatics notes and became too huge.
Instead, I present here a list of confounding vocabulary terms that we all came into the room thinking we knew but instead had different meanings for different people. I also present my own suggested disambiguation for these terms.
| term | Bioinformatics | Microbiology | Epidemiology | Suggested disambiguation |
| Cluster | A group on a dendrogram OR: a set of computer nodes that work together in an environment to facilitate parallelized analysis | A group of related illnesses | Use a prefix: phylo-cluster, epi-cluster, computer cluster | |
| Traceback | The act of finding the last common ancestor for a group of taxa on a tree | The act of finding the common source of a group of cases | I feel like this is just a buzzword and can be replaced. Bioinformatics: state that you are finding the last common ancestor. Public health: state that you are finding the common source. | |
| Related | When two genomes or genes are genetically similar | When two organisms are similar using some typing scheme (e.g., serogrouping, PFGE, etc) | When two cases of infected individuals are similar (e.g., by the food they ate, by their geography, etc) | If it's unclear, I prefer to use "phylo-related" or "epi-related" or something similar |
| Coding (via homologous) | Computer program | Where a gene gets turned into a functional unit | A way to categorize public health events such as outbreaks | Context. Use it in complete sentences! |
| Mapping | Assigning sequence reads to where they match on a reference genome | geographic information system | Again, context | |
| (phonetic ambiguity) GUI or gooey | A graphical user interface | Something a little bit gross | Context is probably your friend here |
Are there any other terms to bring up? Please list them here in the comments!
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