I'm looking for biological datasets with specific properties that are available for me to analyze. Informally put, I have a hammer and I am looking for a nail. That is to say, I have an algorithm and I am looking for suitable data to test if it can tell us anything interesting about biology. Let me start by characterizing the properties that I'd like this data to have.
The data must be representable as signed directed graphs, which in less formal terms means that I am looking for a network where the connections between the nodes are arrows with a +/- sign associated with them.
The signed property of the edges must represent a property of the relation between discrete objects that only takes on one of two values. One way to get signed values from quantitative data would be to use the sign function, keeping only the relations whose sign of the quantitative variable were not equal to zero. Another way is to encode Boolean values, where False is - and True is +. I'd like to further clarify that the data should not only conform to this criteria, but should have instances of both positive and negative paths within the data.
The directed property of the edges mean that we care to distinguish 'A relates to B' from 'B relates to A'; order matters. Both, one, or neither of these relations can hold in these networks between any two nodes A and B.
The data must be analyzable in the sense that I can obtain the data in a form where I can either (1) immediately analyze the data or (2) transform/manipulate the data into a form that I can analyze. As a computer programmer, I'm likely to be able to find packages for (or code for myself) moderately arbitrary transformations as long as they are computable and interpretable. That is to say, in your answer I would like you to not worry too much about whether you have a ready-to-use software solution for analyzing or transforming the data. What I would like considered is whether there is (1) a direct download for a/the datafile(s) or (2) an application programming interface (API) for downloading the data in either pieces or as a whole.
Preference will be given to answers that do not cost money, and do not require creating accounts (although either are acceptable).
All else being equal, I'd prefer larger datasets (n > 1000) over smaller ones.
Preference will also be given to answers where the dataset has additional variables are available on the vertices. For example, if the vertices represent genes, then additional variables on the vertices would mean more data is available that describe those genes.
The dataset(s) should be citable.
While I'm open to other biological subjects, there are two biological topics that I feel should be representable in the mathematical way I've described above.
The first is gene regulation data. The vertices would be genes, and for any two genes A and B we could have any of the following relations
- Gene A downregulates Gene B
- Gene A upregulates Gene B
- Gene B downregulates Gene A
- Gene B upregulates Gene A
The second example I've thought of is in biological signaling as the signals are sometimes directional (sender to receiver) and might have some sort of sign (turn on/off, increase/decrease).
Bonus points if the data is topical (COVID-19/coronavirus-related for example).
I've downloaded a few datasets from BioGrid, but I didn't see the kinds of mathematical properties I was looking for in those datasets. If there are datasets here that you think meet my criterion, please mention them.