Colil : HELP

Colil

In life sciences papers, citations are widely used and typically consist of two parts: a) a list of references found at the end of the citing paper that provides full bibliographic information for each source; and b) reference markers located in the text that are linked to the references. The text surrounding a reference marker is defined as the citation context. In citation contexts, researchers must clarify the relationships between their paper and the papers cited within their paper. However, this process may be difficult for some researchers, especially for non-English-speakers. In such cases, these researchers can learn how to write citation contexts more efficiently by observing the citation contexts that other researchers have made on a paper. For this purpose, we developed the Colil (Comments on Literature in Literature) database and a web-based search service called Colil for citation contexts in the life sciences domain. The data needed for the Colil database have been extracted from open access papers deposited in PMC Open Access Subset (PMC-OAS). Colil searches for a cited paper in the Colil database and then returns a list of the citation contexts for it and its relevant papers based on co-citations. We also expect that a set of citation contexts retrieved from Colil for a give paper should help researchers to comprehend the paper more efficiently. Users also query and browse the Colil database using the common query interface (SPARQL) through our SPARQL endpoint. Furthermore, complete dumps of the Colil database are downloadable through the FTP site.

Quick start

To identify a target paper, you can input a PubMed ID directly or keywords.

Input a PubMed ID of a target paper into the [PubMed ID] box. After that, hit the `enter` key. You can try PubMed ID '10592235' as an example paper by clicking the `Try : 10592235` button.
Input keywords into the [KEYWORDS] box. After that, hit the `enter` key. Colil searches for papers using the PubMed search API, and then the hit papers are displayed in a modal dialog. In case of no matches, you will get a message indicating so. Each hit result contains the bibliographic information including title, authors, journal, year, volume, and issue. You can choose one of hits, and then Colil returns the corresponding result on the main page. You can try keywords 'iPS 2006:2008[dp] "Cell"[jour]' as an example keywords by clicking the `Try : iPS 2006:2008[dp] "Cell"[jour]` button.

You will get citation contexts and co-citations if your query matches the Colil database as a cited paper. Colil's main page is divided into three parts, described below.

(1) Bibliographic information about the hit cited paper

The corresponding bibliographic information of the hit cited paper is shown. It includes title, authors, journal, year, volume, issue, and PubMed ID, and the title is anchor text that links to the corresponding PubMed page.

(2) Citation contexts for the hit cited paper

In the table, each row shows the citation context which cites the hit cited paper.

In cell of links, there are three links.
1. Colil link : link to the corresponding Colil page
2. PubMed link : link to the corresponding PubMed page
3. PMC link : link to the corresponding PMC page
title : title of the row paper which cites the hit cited paper
section name : name of the section which contains the citation context
citation context : citation context which cites the hit cited paper (reference markers are highlighted in yellow)

(3) Relevant papers for the hit cited paper

In the table, each row shows the relevant paper which is co-cited with the hit cited paper.

relevance score : relevance score is equal to the number of citing papers
title : title of the row paper which is co-cited with the hit cited paper * Each title is anchor text that links to the corresponding the Colil page
PubMed link : link to the corresponding PubMed page

* Please refer to the FAQs section about co-citation and relevance score for further details.

You have the following options to do next.

Change the number of hit results shown per page
The list box [Entries Per Page] on the upper side of a result table of citation contexts is to choose the number of results shown per page from the following options: 20, 40, 60, or 100.
Change the order of the hit results
The list box [Sort by] on the upper side of a result table of citation contexts is to choose the order of the rows from the following options: "pmid", "title", or "section".
- pmid : sort rows numerically ascending order by PubMed ID
- title : sort rows alphabetically ascending order by paper title
- section : sort rows alphabetically ascending order by section title
Show a SPARQL query to obtain citation contexts for the hit cited paper
If user click the anchor text of “Show query” at the upper side of the table of citation contexts, the Colil shows the corresponding SPARQL query to obtain the table data from our SPARQL endpoint. You can show an example query of PubMed ID '10592235' by clicking the following `Show query` button.
Show a SPARQL query to obtain relevant papers for the hit cited paper
If user click the anchor text of “Show query” at the upper side of the table of relevant papers, the Colil shows the corresponding SPARQL query to obtain the table data from our SPARQL endpoint. You can show an example query of PubMed ID '10592235' by clicking the following `Show query` button.

URL specification

Shows citation contexts and co-citations where a given query matches the cited paper in the Colil database

/browse/papers/PubMedID/Page/NumberOfCitations/SortBy: PubMedID = PubMed ID of the cited paper; Page = page number; NumberOfCitations = # of citation contexts shown per page; SortBy = a sorting order of the citation contexts by following options: "pmid", "title", "section"
(Examples)
http://colil.dbcls.jp/browse/papers/10592235/1/20/pmid
http://colil.dbcls.jp/browse/papers/10592235/1/100/title

FAQs

What do the relevant paper and relevance score mean?

If a pair of papers was cited by at least two papers, we counted it as a co-citation. The relevance score was equal to the number of citing papers. In the case where the papers (A, B) are co-cited by three different papers (X, Y, Z), the relevance score is 3.

How many papers have been published each year in PMC-OAS?

This figure shows the number of PubMed-indexed papers published each year in PMC-OAS (as of March 2014). It has grown over the past 10 years, with the most recent years showing an exponential growth.

How many papers are cited from PubMed indexed papers in PMC-OAS

As of March 2014, there are 545,147 PubMed-indexed PMC-OAS papers that cited at least one PubMed-indexed paper; the obtained papers were distributed across 3,171 journals. The papers contained 24,684,765 citation contexts, and each of them cited an average of 41.5 PubMed-indexed papers. Conversely, 5,136,741 PubMed-indexed papers have been cited by at least one PMC-OAS paper; the cited papers correspond to approximately one-quarter of the entire PubMed entries and are distributed across 11,588 journals.

What is the URL of Colil SPARQL endpoint?

The URL of Colil SPARQL endpoint is "http://colil.dbcls.jp/sparql".

Please refer to this page for sample queries.

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.

support AT dbcls DOT rois DOT ac DOT jp

DBCLS

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