Re: IDO issues (from the perspective of the Apollo project)

[Asiyah Yu Lin]

This discussion about the transmission process may need more domain expertise to be involved.

The term I found in the Pathogen Transmission Ontology is defined as such:

transmission process: A process that is the means during which the pathogen is transmitted directly or indirectly from its natural reservoir, a susceptible host or source to a new host.

http://bioportal.bioontology.org/ontologies/PTRANS?p=classes&conceptid=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FTRANS_0000000

This definition doesn't specify the host must be from same species. Whether or not the transmission will lead to an infection was not defined in the definition.

I think the term 'infection acquisition'  as defined below could be the child term for 'transmission process'.

Best,

Asiyah

On Sun, Oct 26, 2014 at 3:01 PM, Mathias Brochhausen <mbroch...@gmail.com> wrote:

Exactly. I agree with Bill. One thing that came up during the call is that in our definition of infection acquisition is to which extend the fact that the textual definition talks about reproduction is creating ambiguity with respect to the infection per se.

"The biological process of pathogen organism(s) entering (the body of) a host organism from a contagious host or a contaminated thing and reproducing using host resources"

I think this could be easily fixed.

Best,

Mathias

On Sun, Oct 26, 2014 at 1:05 PM, Bill Hogan <hog...@gmail.com> wrote:

The reason we called the process 'infection acquisition' in Apollo was to highlight the fact that the infectious host does not undergo any change, only the susceptible one that acquires an infection.

So in Apollo for sure, we decided that transmission occurs only when it results in an infection.

What is the plan for capturing the discussion to date?  IDO itself, or also its documentation?

Bill

On Sun, Oct 26, 2014 at 10:48 AM, Mathias Brochhausen <mbroch...@gmail.com> wrote:

Hi,

so following Alan's suggestion I'll make the start in continuing the discussion via e-mail.

I have to go back to something we already discussed during the call and I am fully aware that this is an issue that needs to be discussed with the Transmission Ontology:

During the phone call it was suggested to propose to Lynn to change the definition of transmission process to something along the line of:

"A pathogen transmission process in which a pathogen is transmitted from one host to another."

re-using formulation for the definition of 'horizontal pathogen transmission process".

I'd hold that the definition could be optimized. The definition doesn't actually say what a transmission is (what necessary parts it has, etc.), but it uses the verb transmitted to define the transmission process, which seems a little bit circular to me.

Question that might help writing the definition are:

Is transmission only about re-location of pathogens?

Do we only talk about a transmission when it results in an infection?

Maybe I am overlooking something…

Best,

Mathias

On Thu, Oct 23, 2014 at 10:19 AM, Lindsay Cowell <Lindsay...@utsouthwestern.edu> wrote:

Thank you Alan for the thoughtful response.  I agree with all of Alan’s comments.

Lindsay

From: Alan Ruttenberg <alanrut...@gmail.com>
Date: Thursday, October 23, 2014 at 10:04 AM
To: Mathias Brochhausen <mbroch...@gmail.com>
Cc: Dept of Clinical Sciences <lindsay...@utsouthwestern.edu>, Asiyah Yu Lin <lini...@gmail.com>, Alexander Diehl <add...@buffalo.edu>, Bill Hogan <hog...@gmail.com>, Barry Smith <phis...@buffalo.edu>, Albert Goldfain <albertg...@gmail.com>
Subject: Re: IDO issues (from the perspective of the Apollo project)

On Wed, Oct 22, 2014 at 7:05 PM, Mathias Brochhausen <mbroch...@gmail.com> wrote:

I think the meeting went fairly well.

One or two questions/comments:

What is the final vision? Once we eliminated the discord between IDO and Apollo-SV, will IDO also look to re-use Apollo-SV terms that are domain relevant, but not present now?

I will offer only my vision. 

- Once IDO changes are made, If there are terms in Apollo-SV that are duplicative of terms in IDO (i.e. equivalent, but previously not understood to be) then such Apollo-SV terms should be obsoleted and the IDO terms used. 

- if there are terms in Apollo-SV that we agree properly belong in the domain of IDO, we should discuss moving them to IDO, retaining, however, the Apollo-SV identifier, possibly clarified definition, and provenance (term editor, etc). IDO would be, in such agreed-upon-cases, the manager of the term and Apollo-SV would MIREOT it back in. We have discussed, in the technical committee, a mechanism for distinguishing the current managing ontology for a term from the original ontology it was defined in.

- If there are terms that are in Apollo-SV which are closer to being application specific then I would leave them in Apollo-SV

- The revised Apollo-SV would formally become an IDO extension and developers engage constructively to participate (and define) the process of coordination among members of the IDO Consortium. Selected developers might join the IDO effort, if interest was in the broader scope ontology.

 

The elephant in the room is that many definitions (both textual definitions and axioms) revolve around the term IDO:infection once we get the main issues resolved, I need to check whether we can maintain terms for Apollo-SV that are less centered around that term and more centered on the process (which is by and large the approach Apollo-SV took).

I don't think this is a problem, in principle. Once axioms are added that link one to the other then we should be able to have queries that query across both. 

I do think that it would be helpful to have some collaborative discussions with the Apollo-SV team to share experience and discuss whether, in the the light of that experience, it might be more beneficial for Apollo-SV to pay more attention to the OGMS-based formulation. There is a lot of thought that went into OGMS and IDO, and it may be that the Apollo-SV team will discover things they haven't thought of in such a discussion.

YVMV (your vision may vary ;-) (I would be very interested in hearing alternative visions)

Alan

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[Mathias Brochhausen]

Asiyah,

if you don't mind, please take a look at the paper and at the e-mail I sent out recently about the definition of transmission process you refer to.

I think the definition you cite is problematic.The formulation "...is the means during which the pathogen is transmitted..." raises a number of question.

If John kisses Mary and there is a transmission of herpes viruses during that process, is the kiss the transmission process.

I think that is not and should not be what is intended. But that is exactly what the formulation "...the means during which..." would allow.

[as a footnote: this formulation also seems to make a ontological commitment where process have roles/functions. At least that is how one process being the means of another could be understood (without stretching the meaning of those words)]

In the e-mail I sent out recently, I also raised the question of a formulation like ""A pathogen transmission process in which a pathogen is transmitted from one host to another." (which was a solution we discussed during the call) is not really defining what transmission is, since the definition itself uses the verb transmits".

Best,

Mathias

[Lynn Schriml]

Hello Asiyah,

  I would be happy to help clarify here. 

These transmission terms come from my pathogen transmission process ontology. 

  In the ontology, we did not specify who/what was the host, to keep this description as

generic as possible.  As we were only describing the transmission itself, not the effects of the transmission

nor who/what was involved specifically. 

In IDO further subtypes, as you suggested may be appropriate, as we do not define if infection is the outcome of the

transmission.

I hope this helps.

Cheers,

Lynn

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[Lynn Schriml]

Hello Mathias,

   I wasn't involved in the earlier discussion, 

however, I thought it might be informative to know the 

source of the terms/concepts in the ontology.

The CDCs Introduction to Epidemiology, outlines

on page 45 the modes of transmission. 

http://www.facmed.unam.mx/deptos/salud/bibliotecav/epi_course.pdf

Cheers,

Lynn

[Mathias Brochhausen]

Lynn,

sorry, yes, I wasn't aware that the e-mail went out to a larger group. 

Thanks for the link that is indeed very useful to know.

Best,

Mathias

[Asiyah Yu Lin]

Hi Mathias,

I understand your point about using 'transmit' to define 'transimission'.

If you have some proposal, why not write it down.

After all, Lynn is the person who govern the PTRANS ontology, if I am right.

She may adopt your definition.

Best,

Asiyah

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[Mathias Brochhausen]

Hi Asiyah,

I am willing to work towards a better definition, but I doubt that I can do that alone.

In the previous e-mail I sent out two questions that I think need to be answered to write the definition.

For simplicity sake, I just copy and paste my entire message:

"Hi,

so following Alan's suggestion I'll make the start in continuing the discussion via e-mail.

I have to go back to something we already discussed during the call and I am fully aware that this is an issue that needs to be discussed with the Transmission Ontology:

During the phone call it was suggested to propose to Lynn to change the definition of transmission process to something along the line of:

"A pathogen transmission process in which a pathogen is transmitted from one host to another."

re-using formulation for the definition of 'horizontal pathogen transmission process".

I'd hold that the definition could be optimized. The definition doesn't actually say what a transmission is (what necessary parts it has, etc.), but it uses the verb transmitted to define the transmission process, which seems a little bit circular to me.

Question that might help writing the definition are:

Is transmission only about re-location of pathogens?

Do we only talk about a transmission when it results in an infection?

Maybe I am overlooking something…

Best,

Mathias"

Best,

Mathias

[Asiyah Yu Lin]

Hi, Mathias,

As for the second question,  my opinion is that transmission is not only process that leads to an infection, which is captured by  'infection acquisition' in Apollo.

I am not sure about the first question.

Best,
Asiyah

[Lynn Schriml]

No problem.

I am happy to contribute to the conversation.

Cheers,

Lynn

Sent from my iPhone

[Lynn Schriml]

Hello Mathias and Asiyah,

I am all for a better definition.

To address the questions, transmission is all about the movement of the pathogen, and the ontology is describing the methods by which the pathogen is being transmitted. (Transmission method)

These transmission methods are straight out of the CDC epidemiology book. 

And these methods of transmission is  described without any connection to infection. 

Cheers,

Lynn

Sent from my iPhone

[Mathias Brochhausen]

Hi,

excellent. That is a very good starting point.

Best,

Mathias

[Sivaram Arabandi]

Hi all,

Jumping in a bit late into this discussion with my 2 cents…

There was extensive discussion around this topic within the IDO forum in the past. A quick search on the google groups page showed 11 threads (not including this one). Topics included

- infectious disease vs transmissible disease

- cancer (e.g. in cases of organ transplant)

- transmission types - horizontal, vertical, food-borne, air-borne, etc.

…. and more.

In some ways feels like we are starting over again!

cheers

Sivaram

[Mathias Brochhausen]

Sivaram,

thanks. I am sure that looking at those threads will help finding a better textual definition for transmission (if we agree that is needed [s.b.]).

Just to make sure we are all on the same page: This is not about reopening any discussion.

The question at hand is plain and simple of whether the current textual definition of transmission process (I am refraining from sending it yet again, because I already sent it out twice) is the best we can do.

If there is general agreement that it is, excellent. I won't be a bother any longer.

Best,

Mathias

[Lindsay Cowell]

I agree completely