Talk:Computational genomics

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Molecular Biology: COMPBIO

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First Usage Discussion

Removed from main page for "rv unreferenced assertion about "first usage" of the term: please provide a better reference than a link to a conference website, see WP:V" by User:Tarinth

The first scientific meeting that distinguished this area of science as separate from Biology or Bioinformatics was the 1st Annual Conference on Computational Genomics, 1998 (The 9th installment was held in 2006 [1]). Jethero^Talk 00:03, 3 April 2007 (UTC)[reply]

Also, note that "If you want to request a source for an unsourced statement, consider moving it to the talk page." is from WP:V also.

Thanks for your kind reminder. However, the reference is valid evidence that a society or group with the namesake of this article does indeed exist and it is in the 9th year in 2006. Think of it this way, if you will: Until someone comes forward with a better reference for first use, this is the best we've got. Leave it as a challenge to see if someone can come up with a better 'first use' date, at which point it will be replaced.

Will you accept a reword to:

The first meeting of the Annual Conference on Computational Genomics was in 1998 (The 9th installment was held in 2006 [2]), providing a forum for this speciality and effectively distinguishing this area of science from the more general fields of Genomics or Computational Biology. Jethero^Talk 00:03, 3 April 2007 (UTC)[reply]

And:

The first use of this term in scientific literature, according to [MedLine] abstracts, was just one year earlier by A. Wagner in Nucleic Acids Research "A computational genomics approach to the identification of gene networks." Nucleic Acids Res. 1997 Sep 15;25(18):3594-604. ISSN:0305-1048

(I pre-concede that this is not a comprehensive search, but it is verifiable and true and interesting for now) Jethero^Talk 00:03, 3 April 2007 (UTC)[reply]

I don't feel it's appropriate to allude that advancements in early Bioinformatics or simply 'biology' are attributable to this field, even if they do lay the foundation. Perhaps interesting historical moments would be when and how this field differentiated from other related fields. Otherwise your efforts here might be appreciated instead on the fledgling Computational biology page. Jethero^Talk 00:03, 3 April 2007 (UTC)[reply]

I'm not trying to be difficult, it's just that a statement of first usage needs to be fairly well sourced. I'm certainly in favor of having the information, if possible. Is there a secondary source that can be used to validate the first use you're suggesting? (The problem is that searching through Medline for the first thing you can find is really a form of WP:OR). Tarinth 00:40, 3 April 2007 (UTC)[reply]

I realize you are trying to be diligent, and I'm trying to also learn how to do this properly, so we have only a legitimate and friendly conflict, not a dispute. I've actually tried a few searches online, but was unable to find anything remotely related to 'first use' for this term (or related terms, for that matter), but it is a fair assumption that it was not a word from centuries ago (I don't have a reference for this :) ). In fact, there are very few documents that I can find that use the term that are actually dated. I also know there is a confusing plethora of terms or 'fields' related to biology information processing and data analysis that try to distinguish themselves as separate 'fields' and I think it's important to do so clearly, if we can (i.e. the article is stronger now that there is reference to an actual conference/society and a body of literature). I concede that the medline search as a method to establish first-ever use could be considered WP:OR, in a very strict sense, and possibly primary source rather than secondary or tertiary. However, thanks to your suggestion we no longer claim first-ever use. Perhaps you can suggest a rephrase that would not claim first use, but that would also not tone down the sourced fact that the term was mentioned in a paper in 1997. Note, something like 'the term was used in paper X in 1997' is not very notable and doesn't explain why we included that fact. I am not an expert on WP:OR, but it also seems to me that noting the first use of the term in a medline indexed paper is a statement of fact that is easily verifiable by anyone (i.e. obvious, akin to common sense, akin to not even technically needing a reference, but one is included for people not familiar with medline), rather than something that needs to be peer reviewed (like original research would). Jethero^Talk 03:40, 12 April 2007 (UTC)[reply]

Note also, in Online Etymology Dictionary 'computational genomics' and even 'genomics' don't exist (yet). On Word Spy they are also not indexed, but genomics is 'used' on a page called proteome. Jethero^Talk 03:40, 12 April 2007 (UTC)[reply]

As noted below I don't think there is any reason to have a "computational genomics" page *and* a "bioinformatics" page. The former is included in the latter. Nobody that I know who does bioinformatics would avoid looking at genomes, and no-one who does computational genomics would claim that they are not doing bioinformatics. The fact that there is a meeting called "computational genomics" does not distinguish the field from bioinformatics, it just means that meeting had a genomic focus, which is appropriate since the first whole genome sequences appeared around the same time. However it is in no way a separate field, and having two pages is potentially very confusing. Ian Henty Holmes (talk) 19:52, 22 January 2010 (UTC)[reply]

Definition of Computational Genomics

Reference 2 states:

Computational genomics focuses on understanding the human genome,
and more generally the principles of how DNA controls the biology
of any species at the molecular level.

Which does not seem to have anything to do with:

Modern genomics has been defined in many ways:
 The study of genomes. 
 The molecular characterization of all the genes in a species. 
 The study of genes and their biochemical function in an organism. 
 The comprehensive study of the interactions and functional dynamics of whole sets of genes and their products. 
 The study of the genome and its significance to pathology and disease. 
whichever definition we choose, it is impossible for genomics to achieve
its fundamental goals without the use of advanced   computational tools.
The computational aspects of modern genomics go under the name "computational genomics."

in fact, by this reference, 'Genomics' is defined as a area of inquiry in biology, and 'computational' describes the tools this group uses to address 'genomics' questions. Other claims to the definition are unsourced....therefore, rephrasing Jethero^Talk 03:49, 12 April 2007 (UTC)[reply]

Bioinformatics

What seperates this field from Bioinformatics? —Preceding unsigned comment added by ZayZayEM (talk • contribs) 08:02, 6 November 2007 (UTC)[reply]

I think this is a very good question. To my mind this page provides absolutely nothing that is not already included in bioinformatics. "The study of deciphering biology from genome sequences using computational analysis" is clearly a part of bioinformatics; there is no need to distinguish it with a separate page. I find this page completely redundant. Ian Henty Holmes (talk) 19:48, 22 January 2010 (UTC)[reply]

Bioinformatics, comp biology/genomics can encompass quite a range of activities. My view (and I think it's pretty common, though I can't point to any formal survey) is that "computational biology" is synonymous with "bioinformatics", though the stubby comp biology page frames it as being more about modeling and simulation, akin to systems biology (which is not mentioned on the comp biol page, but is noted on the bioinformatics page, pointing to "computational systems biology" which redirects to Modelling biological systems).

Comp genomics or genome informatics then would be a genome-centric specialization of comp biol/bioinformatics, but I agree with Ian that it does not represent a distinct field, it's just genome-focused comp biol/bioinformatics, just like there can be a proteomics-focused area.
And systems biology can be added to the mix of fields whose scope is subject to interpretation.
The underlying issue here is that these are all fairly young, evolving, multidisciplinary fields at present. Workers in these fields may describe what they do in different ways for one reason or another, based on their training background, institutional organizational rules, granting agency study section guidelines, marketing tends, etc.
There may be no universal consensus or authoritative source of field definitions that everyone will agree with. The aim of Wikipedia in areas like as this is not to try to give the final answer, but to frame the issue and cite relevant sources with alternative viewpoints.

Here's my proposal: Dedicate the computational biology page to be a place for describing terms for the various fields related to bioinformatics/comp biol and create a new section in the bioinformatics page called "Bioinformatics subfields" that summarizes and point to it. The comp biol page is currently designed like this already. Comp genomics could then be merged into the comp biol page, simplifying its content, some of which is more appropriate for the sequence alignment page. Thoughts? SteveChervitzTrutane (talk) 09:34, 29 January 2010 (UTC)[reply]

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