Evolution of a research field—a micro (RNA) example

Database

Citation data was retrieved from the Web of Science™ (WoS) database (http://apps.webofknowledge.com/), produced by Thomson Reuters (see results section, “database”). Search results from WoS encompassed entries from the WoS Core Collection, comprising Science Citation Index Expanded (SCI-EXPANDED), Social Sciences Citation Index (SSCI), Arts & Humanities Citation Index (A&HCI), Book Citation Index (BKCI), Conference Proceedings Citation Index (CPCI), Current Chemical Reactions (CCR Expanded) and Index Chemicus (IC) (http://images.webofknowledge.com/WOKRS513R8.1/help/WOS/hp_database.html).

Search terms and methods

The WoS database was searched utilising the terms “miRNA” and “microRNA” with the Boolean operator “OR”. Upon analysis of initial search findings, conflicting results were identified, namely publications containing the following: mirna estuary, mirna bay, mirna river, mirna equation, Mirna A (author) and mirna SC. As such, the Boolean operator “NOT” was utilised to exclude these findings and refine our search results. Further to this, the research category of “Agriculture” was excluded from our search, as several inaccurate search results were identified within this classification.

Although recognised as the first miRNAs discovered, the initial publications pertaining Lin-4 and Let-7 did not utilise the terms microRNA or miRNA (coined in Ruvkun, 2001), as such these papers did not feature in the search results. To account for this, the Web of Science Core Collection database was searched for Lin-4 and Let-7 in isolation, utilising the Boolean Operator “NOT” to exclude miRNA and microRNA, so as to prevent overlap with original search results.

The publication timeframe analysed encompassed January 1993 to December 2013. Publications of all languages were accepted, comprising all peer-reviewed articles, including reviews, letters to the editor and editorials.

Data analysis

WoS data tools were utilised to perform certain elements of result analysis e.g. generating Journal Citation Reports. Additional data analysis was performed using Microsoft Excel 2010© and Minitab version 16 ^®.

N.B. The results returned from WoS upon searching study criteria were found to increase with the passage of time. This is thought to be due to delayed indexing of journals among other factors. As a result, some figures containing quantitative numbers may differ slightly among sections of this manuscript, when totalled.

Database

Several research platforms currently exist for examining bibliometrics, including the Web of Science™, Highwire© and PubMed™. Prior to commencing this study, the suitability of these databases was individually analysed to allow selection of the optimal data resource. Ultimately, WoS was chosen for the purpose of this study due to superior journal coverage, approximately 9,300 compared to HighWire (1,700) and PubMed (5,669). An additional significant factor was the return of a substantially higher proportion of results using the defined study search criteria (see section ‘Search terms and methods’).

Publication distribution

The number of published items identified pertaining to miRNAs, as catalogued in the Web of Science™ Core Collection database (1993–2013), totals 26,177 publications. The first publication occurred in 1993, with minimal additional publications (35) until 2003 (Fig. 1). Sixty-two percent of all miRNA literature (16,348 publications) was published within the period 2011–2013 inclusive. Currently, the highest output occurred in 2013, with 25% of total miRNA publications (6,560). Of total publications identified, 99.2% of items were published in English (25,980 publications), with the remainder of articles in French (49 publications), Chinese (46 publications), German (38 publications), Spanish (17 publications), Polish (14 publications), Japanese (9 publications), Czech (2 publications) and Hungarian (2 publications) (Fig. 2).

Publications by country

To further analyse miRNA-related literature, the distribution of publications by country was determined. In total, 84 countries contributed to the miRNA literature, as outlined in Table 1 (Top 25). The top 5 most prolific countries account for 83% of total publications (21,652). The USA is responsible for 42% of all miRNA literature (11,056 publications) followed by the Peoples’ Republic of China 21% (5,584 publications), Germany 8% (2,083 publications), the United Kingdom (1,527 publications) and Japan 6% (1,474 publications). Further nations featuring within the top 10 most prolific countries include Italy 6% (1,455 publications), Canada (904 publications), France (848 publications), Australia (650 publications) and South Korea (645 publications) (Fig. 3). Interestingly, separating the United Kingdom into its constituent countries England alone would rank 6th (1,239 publications) behind the USA, the Peoples’ Republic of China, Germany, Japan and Italy (Fig. S1).

Research categories

Analysing the ontological research categories by which miRNA publications are classified in the WoS database, the top 50% of miRNA publications identified can be categorised into medicine and health sciences, which comprises of Biochemistry Molecular biology (23.5%, 6,163 publications), Oncology (15.5%, 4,070 publications), Cell biology (15%, 3,923 publications) and Genetics heredity (10%, 2,554 publications) (Table 2). Further ontological categories of miRNA research listed include horticulture, marine science and entomology.

Peer-reviewed publications

The categories of research, as defined in Table 2, are comprised of miRNA publications that feature in various international peer-reviewed journals. Table 3 outlines the 25 most prolific journals publishing miRNA research (Table S1, 50 most prolific). In the 20 year period analysed, the youngest journal Public Library Of Science ONE (PLoS ONE) delivered the largest number of miRNA-related publications at 1,589 (6% of total), with Nucleic Acids Research responsible for 489 publications (2% of total) and Proceedings of the National Academy of Science of the USA (PNAS) 451 publications (2% of total). We found the top 50 journals were responsible for 38% of total miRNA publications, of which the top 10 journals represent 18% of total miRNA publications identified.

Document type

MiRNA publications are comprised of various document types including original articles, review articles, news items, editorial material, corrections, reprints, database reviews, proceedings papers, letters and meeting abstracts. Of the 26,177 publications identified, 69% of all documents were original research articles (18,111 publications). In addition to original articles, 14% of published items comprised meeting abstracts (3,659 publications), 13% review articles (3,314 publications) and 3% were editorial material (647 publications). The remaining publications comprised of a minimal number of article corrections, news items and reprints. Table S2 shows an analysis of published document types for the top 10 journals which published miRNA-related documents. Constant with the overall trend, articles featured most prominently, comprising 88% of publications for these top 10 journals (4,789 publications), followed by meetings abstracts 8% (393 publications), reviews 1.5% (73 publications), editorial material 0.6% (28 publications) and corrections 0.4% (20 publications). Proceedings papers, letters and database reviews comprise the remainder, providing minimal input.

Publication citations

For all miRNA related publications, 837,898 citations were found by querying the WoS Core Collection Database. In concordance with publication numbers, citations per year increased exponentially peaking in 2008, at which point citation rate decreased (Fig. 4A). Ranking the total number of citations by country, publications originating from the USA received the highest total number of citations (n = 475,300) followed by China (n = 72,265), Germany (n = 71,051), Italy (n = 47,084) and England (n = 42,970) (Fig. 4B). Analysing the average citation per item for the top 10 countries publishing miRNA material, the USA retained the first position (44.3 citations per item). However, the remaining positions changed with the second position now held by England (35.9 citations per item) followed by Germany (35.4 citations per item), France (34.4 citations per item) and Italy (34.2 citations per item). Interestingly, of the top ten countries China now displays the least number of citations per item (n = 14.5) (Fig. 4C). Examining the citations per item from the top 20 countries (as described in Table 1), the rankings change considerably with Switzerland (13th) now displaying the highest number of citations per item at 55.1, followed by USA (44.3 citations per item), then the Netherlands (39.6 citations per item), England (35.9 citations per item) and Sweden (35.8 citations per item) (Table S3).

To further analyse the citation pattern, we investigated citations of the top 10 journals publishing miRNA material (Fig. 5). Proceedings of the National Academy of Science of the USA (PNAS) was the most frequently cited with 6% of the total citations (46,112 citations), followed by Cancer Research, Nucleic Acids Research and PLoS ONE each with 3% of total citations (26 763, 26 118 and 20 242 citations respectively). The final entry in this list is RNA A Publication of the RNA Society with 2% of the total citations (19, 217 citations).

Considering citations per publication, Table S4 outlines the 10 most cited miRNA publications since the discovery of this research field. The top 3 publications cited featured in the journal Cell, with an accumulative total of 11,581 citations (1.4% total citations). 6 of the top 10 publications cited featured in Nature, Nature Reviews Cancer or Nature Methods, with one publications featuring in PNAS. The first, seminal, miRNA publication by Lee et al. ranks third (3,671 citations) and the second key miRNA publication by Pasquinelli et al. (2000) features 28th (931 citations). The top 10 cited papers feature over a 16 year period, with three publications in 2005, three in 2006 and one publication in each of the years 1993, 2004, 2008 and 2009. Of this top 10, four items are review articles. To further examine significant miRNA publications, the top 10 most cited primary research miRNA publications were identified (Table 4). Cell was still seen to contribute 3 of the top 10, with Nature, Nature Genetics and Nature Methods contributing 5 publications and PNAS one publication, with the addition of one publication by Science.

Open access versus pay-per-view

Of the miRNA related publications identified, 17% of publications were open access (n = 4, 560), with 83% of publications pay-per-view access (n = 22,788) (Fig. 6A). Analysing the citations of these two categories of publication, open access items were cited 84,864 times, representing 10% of overall citations. However, pay-per-view publications were cited 731,470 times, which represented 90% of overall citations (Fig. 6B). Average citation per publication reveals 32.1 citations per pay-per-view publication, compared to 18.6 citations per item for open access publications (Fig. 6C).

Hallmarks of miRNA research

Utilising the bibliometric data retrieved, we identified the key discoveries in the field of miRNA research. The seminal miRNA publication, outlining the discovery of these short RNA molecules, by Lee, Feinbaum & Ambros (1993) is certainly the first hallmark of miRNA research. Subsequent to this, recognition of conservation of miRNA sequence expression across animal phylogeny from nematodes to humans by Pasquinelli et al. (2000), with the identification of further miRNAs, also represents a significant key advancement in this field. As previously discussed (section ‘Publication citations’), these papers feature 3rd and 28th respectively in the most cited miRNA publications, highlighting their visibility and influence.

Following these crucial findings, discovery of the regulatory roles of miRNAs in various cellular processes, from differentiation to apoptosis, should be considered highly significant in furthering our understanding of the functionality of these short RNA molecules (Place et al., 2008; Filipowicz, Bhattacharyya & Sonenberg, 2008; Bartel, 2004). The next, related key event in the miRNA field was the discovery of deregulation of miRNA expression associated with human diseases, such as cancer (Calin et al., 2002; van Rooij et al., 2006; Schaefer et al., 2007). This discovery raises a potential use of miRNA, as both predictive and prognostic biomarkers of disease. At present, multiple clinical trials are currently registered with ClinicalTrials.gov, investigating the ability of miRNA to function as biomarkers of disease and response to current therapies.

Another key event in the evolution of the field has been the discovery that miRNA are capable of extra cellular signalling (Valadi et al., 2007). This novel finding significantly added to our knowledge of the mechanisms that can be employed for cell–cell signalling and communication.

The most recent development in the field that should be considered significant is the therapeutic use of miRNAs as targeted therapies to modulate disease (Kota et al., 2009). The attainment of personalised disease management via the use of miRNAs is highly appealing, though many obstacles currently remain, including identification of optimal delivery methods, off-target effects and safety.