OReFiL Help

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Comments and suggestions are welcome, please send an email to yayamamo AT cb DOT k DOT u-tokyo DOT ac DOT jp.

What is OReFiL?

OReFiL stands for Online Resource Finder for Lifescience. It facilitates a search for online resources that are introduced in peer-reviewed papers. You can search by MeSH terms or author names in addition to free words. OReFiL extracts all URLs from MEDLINE abstracts and PubMed-indexed BioMed Central full-papers (implementation or availability sections), and indexes them with MeSH terms and author names.

What can users do using OReFiL?

  1. OReFiL returns up-to-date query-relevant online resources that are introduced in peer-reviewed papers.
  2. Users can search for online resources not only by free words, but also by MeSH terms or author names.
  3. Users can easily verify each hit resource by following the links to its corresponding PubMed entry, web pages having a link to that of the hit resource, or papers citing it through the search systems of BioMed Central, Scirus, HighWire Press, or Google Scholar.
  4. Users can quickly confirm the existence of an online resource web page.

How to compose a query

A query can be any words consisting of alphanumerical characters ("a" - "z", "A" - "Z", and "0" - "9"), "-", or "_". So, any punctuation is ignored. OReFiL supports not only a boolean based search, but also a language-model based search, which utilizes probabilistic inference. Boolean-based and language-model based searches are mutually exclusive. If you submit a query without a boolean operator, such as #band (described below), OReFiL carries out a language-model based search, and with a boolean operator OReFiL carries out a boolean-based search. For example, a query for a language-model based search is: apoptosis caspase, a query for a boolean based search is: #band(apoptosis caspase). Any word can be modified using modifiers such as .mesh (described below) to specify a context of where the word appears, such as in an author name or a title/abstract.

How to use modifiers

The following modifiers can be used to specify a context. Each modifier can be added just after a word with the delimiter '.' (period). For example, if you want to search for any online resources whose corresponding MEDLINE abstracts (including titles) contain the word pathway, you can add the modifier tiab, so, the query is pathway.tiab.

How to use operators

OReFiL uses Lemur Toolkit (Indri). Although the query language can be learned in detail at the original website the use of four rich operators that might be frequently used is explained here. The basic rule is that many operators begin with "#" and each operator takes arguments between brackets. A combination of operators, such as #band(metabolic pathway #1(Computational Biology).majr) is also acceptable.

What does it mean when the title of a search result shows ... ?

How to see the result & what can I do next?

For each entry of the search result, the following information other than the title of the resource is displayed.

When you click 'Show details' the following additional information are displayed.

What is 'Permalink' that shows up for each resource entry?

This is a link to the detailed information of an online resource entry. In addition to the information on the search result page, you can write comments or read comments posted by other users if you login by using OpenID (See 'How to obtain an account')

What is the 'relevance feedback'?

To be precise, the method used in OReFiL's system is known as blind (or 'pseudo') relevance feedback. It raises the ranks of relevant documents that otherwise could not be raised, whose usefulness has been empirically proven. When searching for relevant documents, the system carries out a search process twice, that is, after conducting a normal search, it searches again taking into account of the highly ranked entries of the first result by automatically generating a query for the second search.

Why does not my work show up?

It may be because you did not write down a URL in the title/abstract or the PubMed-indexed BMC paper. Even if that is not the case, we would be glad if you would inform us about your online resource. Send us the URL and PubMed ID pairs along with a pdf file of your publication for which you would feel comfortable being indexed in OReFiL. The email address is yayamamo AT cb DOT k DOT u-tokyo DOT ac DOT jp, thanks.

How to change the sort order

The sort order can be changed in either of the following ways.

  1. Just below the query box there are radio boxes named 'Relevance', 'Updated', and 'Rating'. After choosing one of them, just click the 'SUBMIT' button.
  2. On the right hand of the header showing 'Search Result for "..."', there are two links to the three options 'Relevance', 'Updated', and 'Rating'. By clicking a preferred option, you can change the sort order.

What sort options can I use?

There are three options as follows.

What is the 'Show NEW entries only'?

Checking this box will display only newly added resources on the search result list.

What is the benefit of registering?

If you register and create an account, you can rate or make a comment on a resource.

How to obtain an account to sign in

OReFiL uses DBCLS's (Database Center for Life Science) OpenID account, which can be obtained at https://openid.dbcls.jp/account/signup.

How to sign in

You need to input your DBCLS OpenID in the box at the right hand side of the 'DBCLS OpenID URL:' on the top gray area. After that, just click the 'Sign In' button. You may be requested to input your password by the DBCLS OpenID server.

How to sign out

Just click the 'Sign Out' button on the top gray area.

How to rate an online resource

First you need to sign in. After that, for each resource entry, an item 'Your Rate:' will appear. The rating is on a five point scale, represented by five blank stars. By clicking on each star, you can rate a resource.

How to cancel a rating I did

Click the 'x' button.

How to comment on an online resource

First you need to sign in. After that, for each resource entry, an anchor 'Add comment ...' will appear right next to the stars. Click the anchor and a comment box will show up, where you can make a comment on the resource. Comments can be submitted by clicking the 'SUBMIT' button.

How to modify my comment

Click the anchor 'Edit comment ...' just below the comments on a resource. Edit your comment and click the 'SUBMIT' button.

How to delete my comment

Click the anchor 'Edit comment ...' just below the comments on a resource. Delete your comments in the box, and click the 'SUBMIT' button.

How to read comments submitted by others

Open a resource's detailed information page, by clicking the 'Permalink' anchor. You can read those comments made by others at the bottom of the page.

How to narrow down MeSH terms in the box at the right hand side

Input a word in the box provided and MeSH terms that match the substrings of your input will be shown inside the MeSH terms box.

How to subscribe to a feed of a search result

You can obtain a search result by Atom or RSS (0.91) feeds. The feeds can be viewed in widely used browsers, such as, Windows Internet Explorer or Mozilla FireFox. In addition, you can get the feeds of a search result by the following ways.

How to obtain a list of newly indexed online resources

Newly added resources are available as via Atom/RSS feeds and can be viewed in web browsers or obtained by the following ways.

How to obtain PubMed entries for an online resource

PubMed entries for a resource are available as Atom/RSS feeds and can be viewed in web browsers or obtained by the following ways.

How to get newly added PubMed entries for an online resource

Newly added PubMed entries for a resource are available as Atom/RSS feeds and can be viewed in web browsers or obtained by the following ways.

How to find out when an online resource was last updated

RSS version 0.91 cannot provide information about when an online resource was last updated. To obtain this kind of information, please use Atom.

How to obtain a search result through Web APIs

OReFiL provides REST/SOAP Web APIs. Please see Specification of the Web APIs.

How to obtain information on an online resource through Web APIs

OReFiL provides REST/SOAP WebAPIs. Please see Specification of the Web APIs.

How to change the language setting

You can change the language setting (English or Japanese) by the following ways.

If you do not specify a language code, OReFiL will automatically determines the language setting based on your browser's preference (ACCEPT_LANGUAGE).

I am having trouble using the OReFiL SOAP API from Taverna.

Taverna 1.7.0 or earlier versions have a problem of handling SOAP messages and cannot utilize the OReFiL SOAP API. Please use the latest version.

Who developed/maintains OReFiL?

OReFiL has been developed and maintained by Yasunori Yamamoto, PhD at the Database Center for Life Sciences (DBCLS) (A former member of Takagi Laboratory, Department of Computational Biology, University of Tokyo).