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qfo / OrthologyOntology

Working draft of a common ontology for describing orthology resources
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Questions about Figure 2 #2

Closed olgabot closed 3 years ago

olgabot commented 4 years ago

Hello, Thank you so much for writing up the Quest for Orthologs data and Orthology Ontology. I am rather new to the evolutionary biology/orthology field and working on a paper to compare RNA transcriptomes without the need for defining orthologous gene pairs, so your resources have been invaluable. I only discovered the project online in October of last year, and just missed the 2019 conference, but am hoping to attend the 2021 one!

Since I am an evolutionary biology newbie, I had some questions about Figure 2. I redrew it in my own hands to try and get a grasp of it:

Screen Shot 2020-01-28 at 9 46 12 AM

  1. What do "TBox" and "ABox" mean? I couldn't find these definitions in in the current version of the document.
  2. Is there supposed to be a line from inst:S100P_ANAPL to orth:Gene? Otherwise it is an instance without a class.

Thank you! Warmest, Olga

olgabot commented 4 years ago

It would also be extremely helpful for those new to the field to spell out the species names and/or link to the UniProt species list in the document. I'm not used to the terminology and had to look up ANAPL, FICAL, PELSI, TAEGU to understand what was going on in the figure. Thanks again!

tarcisiotmf commented 4 years ago

Hi Olga,

Thanks for your suggestions! It will be nice to have you on board next QfO meeting. I will update the documentation and improve it as soon as I have time to do so :) .

  1. What do "TBox" and "ABox" mean? I couldn't find these definitions in in the current version of the document? Terminological Box (TBox) (e.g. classes and relations, we can think it as metadata) and Assertion Box (ABox) (e.g. instances, we can think it as the data). More info as follows: https://en.wikipedia.org/wiki/Abox https://en.wikipedia.org/wiki/Tbox

  2. Is there supposed to be a line from inst:S100P_ANAPL to orth:Gene? Otherwise it is an instance without a class. Yes.

For further information how to retrieve these data we recently submit a kind of tutorial here A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL

Thank you very much again for your feedback!

Best regards, Tarcisio.

olgabot commented 4 years ago

Hi Tarcisio, Thank you so much for your response!

  1. Thanks for the definition! I thought they were a evolution/orthology-specific term so I didn't even think to google them.
  2. Good to know!

I'll check out that tutorial. Thanks again!

Warmest, Olga

tarcisiotmf commented 3 years ago

The figures were improved, the common species name is now shown on them. Thanks for your feedback.