The Disambiguated

Disambiguation usually refers to word-sense disambiguation, the process of identifying which meaning of a word is used in context. Disambiguation may also .
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Software integrating Disambiguate available from: Archived source code as at time of publication: Nonetheless, we believe the manuscript would benefit from some minor amendments in order to increase its utility and accessibility to readers. Needs expanded slightly to better set the scene and describe the general approach of read disambiguation. This is something that is clearly missing. If it is literally impossible to compare to a competitor because the software is not accessible, this should be stated clearly as a reason for the lack of comparison in the paper.


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It would be interesting to know how performance is affected by use of highly mutated tumor xenografts. This is arguably beyond the scope of the paper, but warrants at least some mention. We have read this submission. We believe that we have an appropriate level of expertise to confirm that it is of an acceptable scientific standard, however we have significant reservations, as outlined above.

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This paper describes a computational tool for separating sequencing reads from a sample that contains DNA or RNA from two species. This is a necessary pre-processing step for genomic or transcriptomic analysis of patient-derived xenograft cancer models. The approach is based on alignments of sequence reads to the reference genome sequences for the two species in question. The authors have tested their approach on DNA-seq data from publicly available human and mouse exome datasets concatenated to simulate a xenograft sample.

The results presented in Table 1 show very good separation of reads from the two species datasets with only a small percentage of reads being assigned to the wrong species 0. Similar results were presented for RNA-seq data, although here the percentages of incorrectly assigned and ambiguous reads are unsurprisingly higher than for DNA-seq. Use of the alignment scores, and in the event of a tie the edit distance, is a reasonable approach to disambiguate reads and is the method used for BWA and STAR alignments.

Further, the choice of function sum of edit distance, number of reported alignments and number of gap opens is not completely obvious and raises the question of whether the authors have attempted to tune the function, e. I have read this submission. I believe that I have an appropriate level of expertise to confirm that it is of an acceptable scientific standard. National Center for Biotechnology Information , U.

Journal List FRes v. Published online Jan Gray , 2 Justin H. Johnson , 3 and Zhongwu Lai 3. All authors are employees of AstraZeneca. Accepted Jan This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

This article has been cited by other articles in PMC. Abstract Grafting of cell lines and primary tumours is a crucial step in the drug development process between cell line studies and clinical trials. NGS, patient derived xenograft, explant, disambiguation, sequencing. Introduction Xenografts, both cell line and primary tumour, are routinely profiled in preclinical and translational research. Read pairs assigned human hg19 and mouse mm10 by both the disambiguate and xenome algorithms. Open in a separate window.

Methods Implementation The Disambiguate algorithm works by operating on natural name sorted BAM files from alignments to two species. The disambiguation process illustrated.

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Results To illustrate the utility of Disambiguate , raw publicly available human and mouse sequencing data was downloaded. Conclusions In summary, Disambiguate provides an important tool for computationally separating sequence reads originating from two species. Data availability The data referenced by this article are under copyright with the following copyright statement: Software availability Software integrating Disambiguate available from: Notes [version 2; referees: Funding Statement The author s declared that no grants were involved in supporting this work.

Xenome--a tool for classifying reads from xenograft samples. Next-generation sequence analysis of cancer xenograft models. Aligning sequence reads, clone sequences and assembly contigs with bwa-mem. Langmead B, Salzberg SL: Fast gapped-read alignment with Bowtie 2. Approved with Reservations Gavin R. Oliver , Referee 1 and Asha Nair , Co-referee 2.

No competing interests were disclosed. Methodology The methodology should be expanded slightly and made more explicit. Tables should clearly show all numbers pre- and post- disambiguation, rather than having superscripted references in the table legend. Should be more granular, informative and descriptive of the process. Include read alignment etc. Describe the Disambiguate process. Eldridge , Referee 1. Approved Daniel Nicorici , Referee 1.

Editorial Reviews

I have made the following minor observations: If there are several possible choices for parenthetical disambiguation, use the same disambiguating phrase already commonly used for other topics within the same class and context, if any. Otherwise, choose whichever is simpler. For example, use " mythology " rather than " mythological figure ". Naming conventions applicable to certain subject areas are listed in the box to the right; these often contain detailed guidance about how to disambiguate.

Language Policy, Political Theory, and English as a 'Global' Language - Tom Ricento

In particular, for articles about people, see the Disambiguating section in the people naming convention. To conform to the naming conventions , the phrase in parentheses should be treated just as any other word in a title: For common disambiguation words, see User: Users searching for what turns out to be an ambiguous term may not reach the article they expected. Therefore, any article with an ambiguous title should contain helpful links to alternative Wikipedia articles or disambiguation pages, placed at the top of the article using one or more of the templates shown below.

Disambiguation hatnotes are not article content—they are associated with the title, rather than any article topic content. Most hatnote templates generate links automatically, so double square brackets are not normally used within the templates. In some cases there are multiple templates available, one including and another omitting information about the topic of the article. The shorter hatnote may be chosen if omitting the information is not likely to confuse the reader. On a primary topic page for a term that has one secondary topic only no disambiguation page: On a secondary topic page for a term that has one other topic only no disambiguation page: Other variations on these templates are available, including templates for specific subjects such as places, numbers, etc.

Templates are listed and illustrated at Template talk: Otheruses templates example usage. A longer list of disambiguation templates is found at Wikipedia: Many more templates are listed in Category: Disambiguation and redirection templates. A disambiguation page is a non-article page that lists and links to encyclopedia articles covering topics that could have had the same title. The purpose of disambiguation pages is allowing navigation to the article on the topic being sought. The information on a disambiguation page should be focused on getting the reader to their desired article.

A single disambiguation page may be used to disambiguate a number of similar terms. Sets of terms which are commonly so combined include:. Editorial judgement should be used in deciding whether to combine terms in the ways described above. If a combined disambiguation page would be inconveniently long, it may be better to split the disambiguation page into separate pages.

When a combined disambiguation page is used, redirects to it or hatnotes, as appropriate should be set up from all the terms involved. The title of a disambiguation page is the ambiguous term itself, provided there is no primary topic for that term. If there is a primary topic, then the tag " disambiguation " is added to the name of the disambiguation page, as in Jupiter disambiguation. When a disambiguation page combines several similar terms, one of them must be selected as the title for the page with the " disambiguation " tag added if a primary topic exists for that term ; the choice should be made in line with the following principles:.

In addition, when a disambiguation page exists at the ambiguous term, there should also be a redirect to it from the " disambiguation " title; in other words, if "Term ABC" is a disambiguation page, a redirect from "Term ABC disambiguation " should be created if it does not already exist. This type of redirect is used to indicate any intentional links to the disambiguation page, to distinguish them from accidental or erroneous incoming links that should be disambiguated to the appropriate article.

Each disambiguation page comprises a list or multiple lists, for multiple senses of the term in question of similarly titled links. For more information, see the relevant style guide section. For prime examples of disambiguation pages, see Lift and Aurora disambiguation. The purpose of a disambiguation page is to direct a reader seeking information on a specific topic to the right page.

Strictly speaking, entries should be just sufficient for this purpose. It is common to add a little additional information which may make reference to the full article unnecessary. For example, consider the text " Franklin Delano Roosevelt , U. The name only is sufficient in FDR disambiguation for example, to distinguish the president from a flight data recorder. The next phrase, office held and incumbency, is unlikely to be objected to. The rest is unnecessary and inappropriate; it very briefly summarises the article, rather than merely disambiguating.

A disambiguation page is not a list of dictionary definitions. A short description of the common general meaning of a word can be appropriate for helping the reader determine context. Otherwise, there are templates for linking the reader to Wiktionary , the wiki dictionary; see Template: It is also not an interlanguage dictionary; while Geneva is Ginebra in Spanish and other languages, this is not listed in the article, so the Ginebra disambiguation page should not include Geneva.

A disambiguation page is not a search index.

leondumoulin.nl: The Disambiguated (): Steve Fox: Books

Do not add a link that merely contains part of the page title, or a link that includes the page title in a longer proper name, where there is no significant risk of confusion or reference. For example, Louisville Zoo is not included at Zoo disambiguation because people outside Louisville would not readily identify it as the "Zoo", and including all zoos in the world in the disambiguation page is impractical though List of zoos is listed in the "See also" section.

Add a link only if the article's subject or the relevant subtopic thereof could plausibly be referred to by essentially the same name as the disambiguated term in a sufficiently generic context—regardless of the article's title. For instance, the Mississippi River article could not feasibly be titled Mississippi , since that name is used by the U.


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Place names are often divided between a specific and generic part: It is entirely proper to include such place names in disambiguation pages with the specific title North Carolina is properly listed at Carolina disambiguation ; but only exceptionally in the generic title we do not expect to see North Carolina in North disambiguation , just as we do not expect to see Mississippi River in River disambiguation.

To prevent disambiguation pages from getting too long, articles on people should be listed at the disambiguation page for their first or last name only if they are reasonably well known by it. We reasonably expect to see Abraham Lincoln at Lincoln disambiguation , but very few sources would refer to the waltz composer Harry J. Lincoln by an unqualified "Lincoln", so he is only listed at the Lincoln surname anthroponymy article.

This is even more widespread for first names—many highly notable people are called Herb , but typing in Herb gets you an article on plants. Herb disambiguation does not even list any people named "Herb", but instead links to Herb surname and Herb given name , where articles on people named "Herb" are listed. Consensus among editors determines if an article should be listed on the disambiguation page. Include articles only if the term being disambiguated is actually described in the target article.

For example, a use of the term "set" is discussed in the article on Volleyball , so Set disambiguation legitimately includes "Set, the second contact in [[volleyball]]".

disambiguate

Do not add articles to abbreviation or acronym disambiguation pages unless the target article includes the acronym or abbreviation—we are resolving an ambiguity, not making yet another dictionary of abbreviations. If an abbreviation is verifiable , but not mentioned on the target article, consider adding it to the target article and then adding the entry to the disambiguation page.

In particular, do not include people and other things simply because of their initials, unless those initials have been widely used. John Fitzgerald Kennedy is widely known as JFK and this is discussed in the article, so the initials are appropriately disambiguated; however, Marilyn Monroe was never commonly known as "MM", nor was A.

Disambiguation descriptions should not be created for subjects whose only articles are on pages of sister projects, even if the disambiguation page already exists. Do not include references in disambiguation pages; disambiguation pages are not articles. Incorporate references into the articles linked from the disambiguation page, as needed. Do not include external links, either as entries or in descriptions.

Disambiguation pages disambiguate Wikipedia articles, not the World Wide Web. To note URLs that might be helpful in the future, include them on the talk page. An exception is linking to Wiktionary for the dictionary definition of the disambiguated topic. Before constructing a new disambiguation page, determine a specific topic name for all existing pages, and the name for the disambiguation page. Move any page with a conflicting title i. Use the What links here list for the moved page to update pages that link to that page. If an article has been moved to make way for the disambiguation page, use the What links here list of the moved page to access the redirect page created by the move, and replace that redirect page with the new disambiguation page.

Use the new disambiguation page to find and replace see Table of keyboard shortcuts Text editing any existing disambiguation links in existing pages with a link to the new disambiguation page. Note that the standard link templates will actually point to a Term XYZ disambiguation version of the new name. A double disambiguation is a link to a disambiguation page from another disambiguation page. This kind of disambiguation is typically more specific than one with a simplified name. This kind of disambiguation is relatively rare on Wikipedia.

When a more specific title is still ambiguous, but not enough so to call for double disambiguation, it should redirect back to the main disambiguation page or a section of it. This aids navigation, and helps editors to avoid creating new articles under the ambiguous title by accident. Redirects from incomplete disambiguations. For example, Aurora album could redirect as follows where Aurora disambiguation is a disambiguation page:. In some cases, information may be more appropriate as a list than a disambiguation. For example, Cleveland NFL should not be a disambiguation page, but should instead redirect to List of Cleveland sports teams Football.

Pure disambiguation pages should contain interlanguage links only where a similar problem of disambiguation exists in the target language; that is, they should refer to another disambiguation page, not to one of the many meanings from the list. Before moving an article to a qualified name in order to create a disambiguation page at the base name, to move an existing disambiguation page to that name, or to redirect that name to a disambiguation page , click on What links here to find all of the incoming links and repair them.

When repairing a link, use pipe syntax so that the link does not show the new qualifier. A shorter alternative is to use empty pipe syntax, also known as the pipe trick. This allows editors to leave out the piped alternative when editing. Pipe trick for more information. Ambiguous links are periodically checked and repaired, but even if some ambiguous links remain, one of the primary reasons for making a disambiguation page is so that following such links will still be useful to the reader. There is a tool to facilitate ambiguous link repair in the Python Wikipedia Robot.

The bot offers to update links to choices listed on the disambiguation page. Do not forget to seek approval on the Wikipedia: Links to disambiguation pages from mainspace are typically errors. In order to find and fix those errors, disambiguators generate a wide array of reports of links needing to be checked and fixed. Because these reports can not distinguish instances where an editor has made such a link with the intent to point to the disambiguation page, the community has adopted the procedure of rerouting all intentional disambiguation links in mainspace through "Foo disambiguation " redirects.

This makes it clear that such links are intended to point to the disambiguation page. With few exceptions, creating links to disambiguation pages is erroneous. Links should instead point to a relevant article. The purpose of a disambiguation page is to give a list of articles that is likely to include what a reader is looking for when they have typed an ambiguous term into the search box. Disambiguation pages are not articles and so should not be tagged as orphans per the Orphan criteria.

To link to a disambiguation page rather than to a page whose topic is a specific meaning , link to the title that includes the text " disambiguation " , even if that is a redirect —for example, link to the redirect American disambiguation rather than the target page at "American".

This helps distinguish accidental links to the disambiguation page from intentional ones. There is nothing wrong with linking to a redirect instead of linking directly to the disambiguation page; redirects are "cheap" and are basically transparent to the reader. The rule about linking through a " disambiguation " redirect does not apply to redirects to disambiguation pages: Do not create a double redirect, but make a redirect to the disambiguation page directly thus Bill Cox , a redirect from an alternative name, redirects to the disambiguation page and does not go through the redirect William Cox disambiguation.

Although it is permissible for this redirect to be made, it generally should not be linked to in an article for the same reasons direct links to disambiguation pages are discouraged. Redirects to disambiguation pages. Links to disambiguation pages can be displayed in orange in the settings under "Gadgets" by checking "Display links to disambiguation pages in orange". Although disambiguation pages are not articles, a disambiguation page may be listed at Articles for deletion to discuss whether the disambiguation page should be deleted. Disambiguation pages are not articles and should not be categorized as such.

Article categories should lead readers to relevant articles; disambiguation pages should be placed in disambiguation categories only.