HELP

• What is Allie?
• Quick start
• Search options
• FAQs

What is Allie?

Allie is a search service for abbreviations and long forms utilized in Lifesciences. It provides a solution to the issue that many abbreviations are used in the literature, and polysemous or synonymous abbreviations appear frequently, making it difficult to read and understand scientific papers that are not relevant to the reader's expertise.

Quick start

1. Input an abbreviation, a long form, or a substring of either of them into the [KEYWORDS] box. After that, click the `Search` button.
   You can try 'SPF' as an example by clicking the `try "SPF"` button.
   Another way of starting a search is to add a query to URL. The URL http://allie.dbcls.jp/?s=SPF launches the search for long form candidates to the abbreviation 'SPF'.
   Whichever you choose, a query must be at least two characters long.
2. You will get a search result in the order following the default condition if your query matches either abbreviations or long forms ('abbreviations/long forms', hereafter). If your query matches both of them, you will get a page that requires you to choose whether the query is an abbreviation (Abbreviation Search) or a long form (Long Form Search) before displaying the search result. In case of no matches, you will get a message indicating so. In the default condition, results are shown in descending order of appearance frequency of abbreviations/long forms. Each hit result contains the following information:
   
   • Abbreviation(s) or long form(s): If your query matches abbreviations, one of the corresponding long forms will be displayed, otherwise if your query matches long forms, one of the abbreviations will be displayed. In each hit result, appearance frequency of abbreviations/long forms is shown in parentheses.
   • Co-occurring abbreviations: They are the abbreviations that co-occur with the hit abbreviations/long fomrs in PubMed/MEDLINE entries. In the result page, up to three of them are shown, and there is a link to a page showing all of them. The appearance frequency of each abbreviation is shown in parentheses.
   • PubMed/MEDLINE information: Publication year and title of a paper where the hit abbreviations/long forms appear. In the result page, up to three of them are shown, and there is a link to a page showing all of them. In the default condition, they are shown in ascending order of publication year. Each title has a hyperlink to its corresponding PubMed/MEDLINE entry.
3. You have the following options to do next.
   1. Check the next page of the match list if there are more than 30 hit results (30 is the default value, but you can change this setting at the front page).
      Click one of the `Next »` boxes at the upper and lower right of the page. You can return to the previous page by clicking one of the `« Previous` boxes, and also you can go to a specific page by clicking a page number box placed between the previous and next boxes.
   2. Check a list of all the co-occurring abbreviations
      Click the `>> details` button at the co-occurring abbreviations area, and a new page will open. (An example image is here.) Clicking the hyperlink of each abbreviation will display the same search result as you will get when you input one of the co-occurring abbreviations into the [KEYWORDS] box and click the search button.
   3. Check a list of all the PubMed/MEDLINE information
      Click the `>> details` button at the PubMed/MEDLINE information area, and a new page will open. (An example image is here.) In this page, you can see the following information for each PubMed/MEDLINE entry:
      • publication year,
      • title, and
      • abbreviations that appear in the title or abstract.
      Each title has a link to its corresponding PubMed entry.
   4. Change the order of the hit resuls
      You can choose ascending or descending order by alphabet, appearance frequency of abbreviations/long forms, or publication year.
   5. Change the order of PubMed/MEDLINE entries
      You have a sort option of ascending or descending year of publication.

Search options

1. Search method
   • Exact match: Search for any abbreviations or long forms that exactly match a given query.
   • Partial match: Search for any abbreviations or long forms that partly or exactly match a given query.
   Default value is exact match.
2. Sort by
   • Sort order of match entries
     Hit results can be sorted by one of the following ascending or descending orders:
     • alphabetical order of abbreviations/long forms,
     • appearance frequency of abbreviations/long forms, or
     • publication year of papers that contain the abbreviations/long forms in their titles or abstracts
     Default order is by descending appearance frequency.
   • PubMed/MEDLINE entries in each hit result are sorted by publication year.
     You can sort them in either ascending or descending order. Default value is ascending publication year.
3. Show
   You can choose the number of hit results shown per page from 15, 30, 50, or 100. Default value is 30.

FAQs

What do 'cluster(s)' and 'appearance frequency' that appear at the top of the search result mean?

In Allie, conceptually identical abbreviations and long forms are grouped by using a dictionary and an internally developed clustering tool. In the search result, the clustered abbreviations/long forms are displayed as a single hit result and labeled by a representing (most frequently used) name ('cluster label', hereafter) which is shown in the 'Abbreviation/Long Form' column. 'Appearance frequency' refers to the number of clustered abbreviation(s) or long form(s) that appear in a title or an abstract.

Why are there some PubMed/MEDLINE entries that do not contain the cluster label of a hit result?

The clustering method used in Allie is based on conceptual identity, so some expressional variations are accepted within a cluster. As a result, the letter strings of a cluster label may differ from the letter strings of abbreviations/long forms that appear in the PubMed/MEDLINE entry. However, in the PubMed/MEDLINE entry there should be abbreviations/long forms that are conceptually identical to the cluster label.

Is there any publication concerning Allie?

Yes, and here it is.
H. Ao and T. Takagi, "ALICE: an algorithm to extract abbreviations from MEDLINE.", J Am Med Inform Assoc., 2005 Sep-Oct;12(5):576-86.
Full text paper at PubMed Central

How to use REST/SOAP services?

Please refer to this page.

Where is the contact point for reporting a problem or suggestions/comments?

Here is the contact point: support AT dbcls DOT rois DOT ac DOT jp.