I am in the process of creating biological key software tool for use on android devices. I would like to know if there are any established file formats for storing biological key data.


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    $\begingroup$ Could you give us some more details about what you're looking for? Maybe I'm just not familiar with your terminology, but I'm not sure what biological key data is. I work in Bioinformatics and have done some Android development, so I might be able to help you! $\endgroup$ – Kyle. Jan 15 '13 at 15:32
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    $\begingroup$ Dichotomous key? $\endgroup$ – Alan Boyd Jan 15 '13 at 19:01
  • $\begingroup$ Yes, A dichotomous key. apologies for not being more specific. $\endgroup$ – nrhorner Jan 15 '13 at 19:31
  • $\begingroup$ @user521469 The Wikipedia page here points to software which may be a source of file format definitions. $\endgroup$ – Alan Boyd Jan 15 '13 at 19:54

I searched a bit and could not find any such format, but I am not a specialist in taxonomy.

From what I understand, the structure you want is that of either a tree or a DAG (Directed Acyclic Graph). Both are straightforward to store in a variety of formats.

One possibility is to use a format similar to other biological data that has a similar data structure. For example, Gene Ontology is a widely used dataset that has the structure of a DAG and has a number of formats including XML listing the parents and additional data of each node in the graph. See here for their formats.


If you mean some thing like .doc .txt .rar or etc. I think there is no special bioinformatics file formats like that, for example NCBI, EMBL, Expasy and others use this common formats in transfering sequence data. BUT there is some thing called file format for introducing data to this data banks for example FASTA file format:


As you see, a sequence in FASTA format begins with a single-line description, followed by lines of sequence data. The description line is distinguished from the sequence data by a greater-than (">") symbol in the first column. The word following the ">" symbol is the identifier of the sequence, and the rest of the line is the description (both are optional). There should be no space between the ">" and the first letter of the identifier. It is recommended that all lines of text be shorter than 80 characters. The sequence ends if another line starting with a ">" appears; this indicates the start of another sequence. you can learn more things about these bioinformatical formats here and here.

  • $\begingroup$ Thanks for your answer. I am familiar with sequence formats. I was wondering if there was any format for storing data for dichotomous biological keys. $\endgroup$ – nrhorner Jan 15 '13 at 19:32
  • $\begingroup$ Please edit your question. $\endgroup$ – MySky Jan 16 '13 at 10:06

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