Comments and suggestions are welcome, please send an email to yayamamo AT cb DOT k DOT u-tokyo DOT ac DOT jp.
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.
This means our crawler got the HTTP status code of 404 when accessing to the webpage. The probability of its removal is high, although it might be temporal. You can hide those entries by checking the "Hide page-not-found entries" box just below the query box.
This means our crawler could not fetch the webpage when accessing to the URL (the HTTP status code was 5xx). Several cases can be the reason; the server was too busy or down, the net was congested, or the server malfunctioned. So, it might be accessible when you click the link.
This means our crawler could not find a webpage's title or that of what looks like. At least the webpage existed when our crawler accessed.
This means our crawler could not fetch the webpage when accessing to the URL for a reason not listed above. The HTTP status code and the corresponding message follows.
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 one, which utilizes probabilistic inference. Boolean-based and language-model based searches are mutually exclusive. If you type in words without a boolean operator such as #band (described below), the search is language-model based, and vice versa. For example, a search to the following query is a language-model based: apoptosis caspase, and the following one is a boolean based: #band(apoptosis caspase). Any word can be modified using modifiers such as .mesh (described below) to specify a context where that word appears such as in an author name or a title/abstract.
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 OReFiL to search for any entries whose MEDLINE abstracts (including titles) contain the word pathway, you can add the modifier tiab, so, the query is pathway.tiab.
Word w is in MEDLINE titles and abstracts. (Ex. alzheimer.tiab)
Word w is in MEDLINE author lists. (Ex. john.auth)
Word w is in annotated MeSH terms regardless of whether they are MEDLINE entry's descriptors of major topics or not. (Ex. p53.mesh)
Word w is in annotated MeSH terms that are MEDLINE entry's descriptors of major topics or their conceptual ancestors in the MeSH hierarchy. (Ex. p53.majr)
Word w is in annotated MeSH terms that are MEDLINE entry's descriptors of major topics. (Ex. p53.noexp)
OReFiL uses Lemur Toolkit (Indri), and the query language can be learned here comprehensively. Here, I just pick up only three of the rich operators that might be frequently used. A basic rule is that many operators begin with "#" and each operator takes arguments within brackets. Combination can be accepted such as #band(metabolic pathway #1(Computational Biology).majr).
This is the default operator when you just type in words in the query box without any operators. OReFiL searches for query-relevant entries in terms of the language model. Multiple words can be accepted and the word order may matter. An example is #combine(protein protein interaction).
This is the boolean "AND" operator. An example is #band(apoptosis caspase).
This operator takes two arguments and means "filter require", that is, OReFiL searches for entries that match the first argument and ranks them according to second argument as a query. An example is #filreq(Software.noexp #1(sequence analysis)). In this example, OReFiL only considers those resources whose MEDLINE entries have the MeSH term "Software" and rank them according to the query #1(sequence analysis).
This is to be used for OReFiL to regard multiple words as a collocation. You can use this operator regardless of the search models (i.e., boolean based or language-model based). For example, if you want to search for entries that contain the expression "signaling pathway", you need to compose the query #1(signaling pathway).
Those annotated to the MEDLINE abstracts included in the hit list are displayed in the alphabetical order. Each font size of them reflects its frequency in the hit list, so, those terms more frequently annotated in the MEDLINE abstracts in the hit list are bigger, and vice versa. They are only descriptors of major topics. Those MeSH terms also function as a filter to narrow down the search result. By clicking one of them, the browser automatically composes and fills in a required query appropriately. Users can easily add or remove a MeSH term in the query box by clicking the term in the MeSH term box; you do not need to type in a complicated query to narrow down. After confirming the query box, just clicking the "SUBMIT" button is enough to get the result.
For each hit entry, MeSH terms appear below the title of the webpage and its URL. They are those annotated to the corresponding MEDLINE abstract(s). They are descriptors of the major topics.
These links are for checking a kind of "page rank" of the hit webpage, that is, by clicking a link, you can see how many webpages link to the hit webpage. Google and AltaVista provide the link: operator, by which you can get the list of the webpages that have a link to a webpage specified just after the operator. For example, you can search for webpages that have a link to PubMed by filling in the query link:www.pubmed.gov. The assumption is that those webpages to which more webpages have a link are more reputable.
These links are similar to page rank but here each search service (i.e., BioMed Central, Scirus, HighWire Press, and Google Scholar) returns a list of the papers that refer to the hit webpage. So, you can quickly search for those papers, for example, using the tool introduced in the hit webpage.
The title of the papers in which (title/abstract or BMC full-papers) the hit webpage's URL appears. Each is a link to the corresponding PubMed entry.
This is a link to the detailed information of an entry.
In addition to the information on a hit list page, you can read comments posted by other users.
To be precise, I use blind or "pseudo" relevance feedback here. It is a method to raise the ranks of relevant documents 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 first normal search, it searches again utilizing the first result.
It seems because you did not write down a URL in a title/abstract or a PubMed-indexed BMC paper. Even though you wrote down there and the MEDLINE entry does not show up here, we'd be glad if you'd inform us. Also, we're happy if you'd tell us pairs of a URL and a PubMed ID along with the pdf file for which you feel good to be indexed here and that have not been yet. The email address is yayamamo AT cb DOT k DOT u-tokyo DOT ac DOT jp, thanks.
There are two ways as follows.
There are three options as follows.
Checking this box means that only newly added resources are on a result list.
You can rate or make a comment on a resource if you sign in.
You need a DBCLS OpenID to sign in OReFiL, which can be obtained at https://openid.dbcls.jp/account/signup.
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 required to input your password by the DBCLS OpenID server.
Just click the `Sign Out` button on the top gray area.
First you need to sign in. After that, you can see an item `Your Rate:` in each hit entry or each resource's detailed information page. By clicking on a star you want, your can rate the resource.
Clicking the `x` button deletes your rate.
First you need to sign in. After that, you can see an anchor `Add comment ...` just after the stars in each hit entry or each resource's detailed information page. Click the anchor and a comment box show up, where you can make a comment on the resource. Submission is done by clicking the `SUBMIT` button.
Click the anchor `Edit comment ...` just below the comments on a resource.
Click the anchor `Edit comment ...` just below the comments on a resource. Clear off all the words in the box, and click the `SUBMIT` button.
Open a resource's detailed information page. You can read those comments made by others at the bottom of the page.
Input a word you want, and only MeSH terms that have a substring of it can be shown.
You can obtain a search result by Atom or RSS (0.91). Widely used browsers such as Internet Explorer or FireFox can get those feeds. In addition, you can get by the following ways.
Newly added resources can be obtained via Atom/RSS feeds by the following ways.
PubMed entries for a resource can be obtained via Atom/RSS feeds by the following ways.
Newly added PubMed entries for a resource can be obtained via Atom/RSS feeds by the following ways.
RSS version 0.91 cannot provide an update time for each entry. Use Atom that can provide if you need.
OReFiL provides REST/SOAP WebAPIs. Please see Specification of the Web APIs.
OReFiL provides REST/SOAP WebAPIs. Please see Specification of the Web APIs.
You can change the language by the following ways.
If there is no language code in the URL, OReFiL determines depending on you browser's preference (ACCEPT_LANGUAGE).
Taverna 1.7.0 has a problem of handling SOAP messages and cannot utilize the OReFiL SOAP API. Please use a later version.
OReFiL has been developed and maintained by Yasunori Yamamoto, PhD at Database Center for Life Sciences (I was formerly at Takagi Laboratory, Department of Computational Biology, University of Tokyo).