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. 2012 Jun 14;40(Web Server issue):W3–W12. doi: 10.1093/nar/gks632

A decade of web server updates at the bioinformatics links directory: 2003–2012

Michelle D Brazas 1, David Yim 1, Winston Yeung 1, B F Francis Ouellette 1,2,*
PMCID: PMC3394264  PMID: 22700703

Abstract

The 2012 Bioinformatics Links Directory update marks the 10th special Web Server issue from Nucleic Acids Research. Beginning with content from their 2003 publication, the Bioinformatics Links Directory in collaboration with Nucleic Acids Research has compiled and published a comprehensive list of freely accessible, online tools, databases and resource materials for the bioinformatics and life science research communities. The past decade has exhibited significant growth and change in the types of tools, databases and resources being put forth, reflecting both technology changes and the nature of research over that time. With the addition of 90 web server tools and 12 updates from the July 2012 Web Server issue of Nucleic Acids Research, the Bioinformatics Links Directory at http://bioinformatics.ca/links_directory/ now contains an impressive 134 resources, 455 databases and 1205 web server tools, mirroring the continued activity and efforts of our field.

COMMENTARY

‘Because the number of artifacts has increased greatly, it is impossible for many bioinformatics researchers to track tools, databases, and methods in the field—or even perhaps within their own specialty area. More critically, however, biologist users and scientists approaching the field do not have a comprehensive index of bioinformatics algorithms, databases, and literature annotated with information about their context and appropriate use.’ (1)

The need to not only share bioinformatics databases, tools and resources but also compile a bioinformatics ‘resourceome’ has been evident for some time (1). In dedicating a special issue each year since 1993 to new databases or updates and a second issue each year since 2003 to new web server tools or updates, Nucleic Acids Research has successfully created a viable and recognizable dissemination mechanism. Each year since 2005 and extending back to 2003, the Bioinformatics Links Directory has coordinated with Nucleic Acids Research (NAR) to update their community driven ‘resourceome’ with all of NAR’s web server tools (2–8). This coordinated effort has resulted in a comprehensive public repository of bioinformatics tools and databases, annotated with contextual information and organized by functional relevance (http://bioinformatics.ca/links_directory). Users requiring a bioinformatics tool or database for their research may search the Bioinformatics Links Directory using any number of its features, from browsing the biological categories and their drop-down subcategories on the main page, to computing a keyword search from the search box or selecting related links. Content within the Directory is organized by biological subject, with subcategories of common tasks relevant to each subject listed under the corresponding category (Figure 1). A keyword search from the search box (Figure 2) returns links containing the entered keywords found within either the link’s title, description or tag terms—a search for ‘gene set enrichment’ for example returns links containing a Boolean combination of gene AND set AND enrichment, with these keywords highlighted in yellow where they appear in the returned list (Figure 3). Other specific searches may also be computed such as exact word matches using quotation marks. Returned links from a given search may be refined to one or more of the link types within the Links Directory (tools, resources or databases), using the ‘Search Options’ feature (Figure 4). From a link of interest, related or similar links within the Links Directory are retrievable by selecting the ‘Related Links’ tab, where related links are chosen based on the PubMed-related citations feature for the primary link. To aid with determining the usefulness and currency of a link, all links within the Links Directory with one or more citations have a per PubMed Identifier (PMID) and cumulative Google Scholar (9) citation count, as well as a Google+ and Twitter sharing count (10) (Figure 5). A keyword search will return links in descending order of cumulative citation count. Detailed explanations and examples of searching within the Links Directory are provided on the tutorials page at http://www.bioinformatics.ca/links_directory/tutorial. These annotations and search features provide the ‘biologist user with information about a link’s context’ and usefulness so to narrow down the algorithm or database within the Bioinformatics Links Directory ‘resourceome’ best suited to their research need (1).

Figure 1.

Figure 1.

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The homepage of the Bioinformatics Links Directory displays the functional categories and subcategories within which more than 1700 tools, resources and databases are contained. The DNA category is shown expanded into its subcategories.

Figure 2.

Figure 2.

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Searching for links within the Bioinformatics Links Directory may be done through use of keywords in the search box. Suggested search options are provided in the search guide box.

Figure 3.

Figure 3.

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Keyword searches such as for gene set enrichment return matching categories and links, which contain the requested keywords highlighted in yellow.

Figure 4.

Figure 4.

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A returned keyword search may be refined using the Search Options, where returned links may be refined to include or exclude all tools, resources and databases.

Figure 5.

Figure 5.

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All links within the Bioinformatics Links Directory now contain a per PMID and cumulative Google Scholar citation count for the citations listed for each link, as well as a Google+ and Twitter sharing count.

SHIFTING TRENDS

The past decade of NAR Web Server releases has seen significant growth and change in the types of tools, databases and resources being put forth. Although each Web Server issue has seen a steady number of new web servers and updates, the functional utility classification of these web servers has differed greatly over the decade. The Bioinformatics Links Directory in 2006 compiled a graph highlighting the trends in five subcategories of links published by NAR between 2003 and 2006 (3). An update of that graph (Figure 6) shows the exceptional changes in new bioinformatics web servers within these same selected subcategories; Table 1 lists how substantial these changes have been across the entire field of bioinformatics as well (Table 1). Subcategories with active contributions of new web servers in 2006 differ from the subcategories with active contributions of new web servers in 2012 (Figure 6 and Table 1). For example subcategories such as ‘DNA: Tools for the Bench’ subcategory, which contains new web servers for conducting generic DNA analyses such as primer design, exhibited strong growth over 2003–2006 but shows very little growth in 2012 as tools in this category remain relevant over time (Figure 6). In contrast, other subcategories such as Protein: 3D Structural Features have remained active in web server development over time, as the introduction of better technologies and algorithms has permitted a deeper appreciation of proteins and their structural features in 3D (Figure 6).

Figure 6.

Figure 6.

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Number of NAR Web Servers from selected subcategories of the Bioinformatics Links Directory (http://bioinformatics.ca/links_directory/). The number of NAR Web Servers published from 2003–2012 for five selected subcategories of the Bioinformatics Links Directory: Protein: 3D Structural Features; Expression: Gene Regulation; DNA: Tools for the Bench; Sequence Comparison: Analysis of Aligned Sequences and RNA: Functional RNAs is shown.

Table 1.

Historical summary of the number of resources, databases and web server tools listed in each subcategory of the Bioinformatics Links Directory between 2005 and 2012

Name 2005 Total 2006 Total 2007 Total 2008 Total 2009 Total 2010 Total 2011
 2012a
Resources Databases Tools Total Resources Databases Tools Total
Computer related
    Bio-* programming tools 20 20 20 20 20 18 6 12 18 6 12 18
    C/C++ 3 3 3 3 3 2 1 1 2 1 1 2
    Databases 2 2 2 2 3 5 1 5 6 1 5 6
    Java 4 4 4 4 4 4 3 1 4 3 1 4
    Linux/Unix 12 12 11 11 11 10 5 1 4 10 5 1 4 10
    PERL 5 5 5 5 5 5 4 1 5 4 1 5
    PHP 3 3 1 1 1 1 1 1 1 1
    Statistics 9 9 9 9 9 9 2 7 9 2 7 9
    Web development 6 6 2 2 2 2 2 2 2 2
    Web services 5 6 7 7 10 17 3 16 19 3 15 18
    Workflows 3 1 5 6 1 7 8
DNA
    Annotations 29 38 56 57 62 71 1 7 65 73 1 6 59 66
    Databases 56 56 54 2 56
    DNA and genomic analysis 17 19 20 23 24 25 5 1 22 28 5 1 26 32
    Gene prediction 17 32 33 34 37 37 1 1 35 37 1 1 29 31
    Mapping and assembly 12 14 15 15 17 20 3 2 16 21 3 2 11 16
    Phylogeny reconstruction 24 37 43 46 49 53 4 4 45 53 4 4 41 49
    Sequence polymorphisms 22 32 39 41 42 44 1 8 39 48 1 7 39 47
    Sequence retrieval and submission 23 26 30 32 32 30 1 6 23 30 1 7 20 28
    Structure and sequence feature detection 71 118 142 145 150 161 3 10 150 163 3 9 137 149
    Tools for the bench 44 55 63 65 71 76 2 7 67 76 2 4 60 66
Education
    Bioinformatics-related news sources 9 9 9 9 9 9 9 9 7 7
    Community 19 19 24 23 23 18 17 2 19 17 1 1 19
    Courses, programs and workshops 5 5 5 5 5 4 3 3 1 1
    Directories and portals 12 15 15 15 15 18 12 6 18 12 1 5 18
    General 15 15 14 14 14 14 13 1 14 12 1 13
    Tutorials and directed learning resources 9 9 9 9 9 10 10 10 9 9
Expression
    cDNA, EST, SAGE 24 29 36 44 48 49 1 10 38 49 1 8 29 38
    Databases 21 21 20 3 20
    Gene regulation 59 96 119 120 128 138 3 16 127 146 3 16 119 138
    Gene set analysis 11 24 1 29 30 1 32 33
    Networks 8 12 16 2 15 17 1 21 22
    Protein expression 7 8 9 17 22 23 1 3 18 22 1 2 18 21
    Splicing 9 16 19 19 21 22 3 17 20 3 16 19
    Transcript expression and microarrays 54 75 89 101 108 121 5 10 107 122 5 9 96 110
Human genome
    Annotations 22 31 37 38 39 46 2 5 39 46 2 4 35 41
    Databases 31 1 32 30 2 32
    Ethics 7 7 8 8 8 6 5 1 6 4 1 5
    Genomics 4 4 3 3 10 19 3 2 15 20 3 2 16 21
    Health and disease 11 14 19 23 27 29 1 7 23 31 1 7 24 32
    Other resources 22 25 29 29 29 31 9 4 17 30 9 4 16 29
    Sequence polymorphisms 17 25 33 36 38 46 2 4 43 49 2 4 44 50
Literature
    Databases 7 7 7 7
    Goldmines 5 6 6 6 6 5 1 4 5 1 4 5
    Open access resources 2 2 2 2 3 4 1 3 4 1 3 4
    Search tools 6 10 12 12 13 14 6 8 14 6 6 12
    Text mining 7 11 15 22 30 31 4 30 34 4 35 39
Model organisms
    Databases 95 95 94 1 94
    Fish 11 11 11 11 11 11 5 6 11 4 5 9
    Fly 12 16 17 17 17 21 2 8 13 23 1 7 16 24
    General resources 20 23 27 28 29 32 3 12 16 31 3 11 16 30
    Microbes 19 31 38 45 53 60 3 12 49 64 2 9 51 62
    Mouse and rat 28 32 35 35 36 42 4 17 21 42 4 11 24 39
    Other organisms 13 18 21 21 21 22 3 6 13 22 3 4 13 20
    Other vertebrates 10 10 10 10 10 11 1 3 7 11 1 3 7 11
    Plants 11 16 19 21 25 28 2 10 18 30 2 9 20 31
    Worm 9 9 9 9 9 10 1 4 6 11 1 4 8 13
    Yeast 11 15 18 18 18 21 2 9 10 21 2 7 12 21
Other molecules
    Carbohydrates 5 6 6 6 6 7 7 7 5 5
    Compounds 2 6 12 1 14 15 1 15 16
    Databases 26 26 25 1 26
    Enzymes 2
    Metabolites 3 4 7 12 1 12 13 1 13 14
    Peptides 1 1
    Small molecules 1 3 6 6 9 13 2 13 15 2 15 17
Protein
    2D Structure prediction 29 51 58 60 63 65 1 65 66 56 56
    3D Structural features 53 70 75 85 100 1 2 103 106 1 2 107 110
    3D Structure comparison 78 35 45 50 59 71 1 6 68 75 1 6 62 69
    3D Structure prediction 48 59 60 70 83 4 1 85 90 2 1 83 86
    3D Structure retrieval, viewing 28 45 51 52 56 58 4 7 47 58 3 8 42 53
    Annotation and function 26 35 44 47 53 57 5 57 62 5 56 61
    Biochemical features 25 37 40 41 46 46 2 2 43 47 2 2 41 45
    Databases 116 1 117 115 2 117
    Do-it-all tools for protein 6 8 8 13 14 15 3 12 15 3 11 14
    Domains and motifs 50 86 112 115 121 124 14 115 129 14 109 123
    Identification, presentation and format 12 13 14 14 14 14 1 13 14 1 14 15
    Networks & Interactions, pathways, enzymes 48 66 88 94 107 125 3 21 113 137 2 19 113 134
    Localization and targeting 19 30 38 38 39 41 3 39 42 3 34 37
    Molecular dynamics and docking 19 21 27 34 40 1 44 45 1 48 49
    Phylogeny reconstruction 28 36 44 45 53 54 4 5 47 56 4 4 48 56
    Protein expression 7 8 8 8 10 10 1 2 7 10 1 2 8 11
    Proteomics 21 25 27 33 37 39 3 4 32 39 3 4 26 33
    Sequence comparison 7 14 17 18 18 18 18
    Sequence data 7 7 8 9 10 10 1 6 3 10 1 5 3 9
    Sequence features 14 25 31 33 38 46 2 2 46 50 2 3 47 52
    Sequence retrieval 21 27 29 29 31 29 1 6 21 28 1 7 20 28
RNA
    Databases 0 24 1 25 23 2 25
    Functional RNAs 9 14 19 26 32 37 0 5 39 44 5 41 46
    General resources 8 10 10 10 10 11 4 3 4 11 5 2 4 11
    Motifs 9 19 21 22 23 25 0 1 26 27 1 25 26
    Sequence retrieval 11 11 10 11 11 9 0 2 7 9 2 7 9
    Structure prediction, visualization and design 24 38 47 54 58 62 0 3 65 68 3 64 67
Sequence comparison
    Alignment editing and visualization 14 20 21 21 23 25 0 0 25 25 23 23
    Analysis of aligned sequences 27 43 59 60 62 64 0 0 65 65 1 57 58
    Comparative genomics 19 26 33 35 37 48 2 7 40 49 2 6 33 41
    Multiple sequence alignments 19 38 50 56 57 65 1 0 67 68 1 1 62 64
    Other alignment tools 6 11 11 11 11 12 0 0 13 13 12 12
    Pairwise sequence alignments 11 22 23 26 33 35 1 0 34 35 1 30 31
    Similarity searching 13 31 47 47 49 50 1 2 49 52 1 3 45 49
Total unique resources, databases and tools in Bioinformatics Links Directory 700+ 1000+ 1100+ 1200+ 1400 1500 144 480 1250 1874 134 455 1205 1794
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aA complete listing of all URLs listed in the Nucleic Acids Research 2012 Web Server Issue can be accessed online at: http://bioinformatics.ca/links_directory/narweb2012.

Indeed, many of these trends in subcategory activity reflect the introduction of a new research technology and/or an underlying research need. As originally discussed in 2009, yet still evident throughout Table 1, there are observable sharp spikes in the number of informatics tools available in a given biological area or specific to a particular task (6). Although between 2006 and 2007, there was a spike in ‘DNA: Structure and Sequence Feature Detection’, ‘Expression: Gene Regulation’ and ‘Expression: Transcript Expression and Microarrays’ most likely in response to the pervasive use of expression platforms and transcript analyses at that time, current spikes in ‘Human Genome: Genomics’, ‘Sequence Comparison: Comparative Genomics’ and ‘Sequence Comparison: Pairwise Sequence Alignments’ between 2010 and 2012 may be reflective of the introduction of next-generation sequencing technologies. Table 1 highlights all the trends between 2005 and 2012 across all subcategories of the Bioinformatics Links Directory (Table 1) (individual calendar year data are not available for 2003–2005 as the Bioinformatics Links Directory collaboration with NAR began in 2005 for all data before that). Of note are the aggressive coverage of databases, which began in 2011 and the need for additional subcategories such as ‘Other Molecules: Enzymes and Peptides’ in response to the growing diversity and depth in the field.

CONSTANT GROWTH

The number of bioinformatics links produced by the community has nonetheless continued to accumulate over time. When first released in 2002 under Bioinformatics.ca, there were only 385 links in the database. By 2005, when the Bioinformatics Links Directory began its collaboration with NAR, the Directory already contained 700+ web servers and resources (2). The Bioinformatics Links Directory has continued to grow (and diminish in size as web servers become extinct) with each successive year (Table 1). The Bioinformatics Links Directory now contains more than 1200 unique web servers. This year's NAR Web Server Issue introduces an additional 90 web servers and 12 server updates (Table 1). The complete listing of URLs cited in the 2012 Web Server Issue can be accessed online at the Nucleic Acids Research website, http://nar.oxfordjournals.org/, and at http://bioinformatics.ca/links_directory/narweb2012/.

Growth has also resulted in change. In 2011, the Bioinformatics Links Directory introduced all the databases published by Nucleic Acids Research over their 2010–2011 window and completed a major reorganization of its existing links (8). Links were reclassified into one of three types reflecting the growing variety of bioinformatics materials being generated to support research: (i) Resource—a static resource whose intention is to convey bioinformatic information; (ii) Tool—a bioinformatic web server or downloadable software tool that can query, analyze, extract or modify input data and (iii) Database—a biological data store that can be queried. Under this new schema and with this expanded content, the Bioinformatics Links Directory now contains 1794 links comprising 455 databases, 134 resources and 1205 web server tools (Table 1). The Bioinformatics Links Directory has also initiated active curation of its content, removing dead content and correcting content errors, which has resulted in more accurate although occasionally smaller counts for 2012 (Table 1). Over time, the Bioinformatics Links Directory is expected to continue its growth and evolution in keeping with the current pace of research.

FUTURE CHALLENGES

With such a vast number of bioinformatics tools available for biological research, now more than ever, there is a need for a well-annotated and user-friendly ‘resourceome’ (1). In 2011, the Bioinformatics Links Directory introduced features to facilitate peer review of its links and link ownership (8). The application of Google +1 and other social media features, such as Twitter to the Bioinformatics Links Directory, provides users with the opportunity to share useful links; registered users may also post comments and review a link’s usefulness or start a discussion forum. Along with enhanced search capabilities and MeSH term and keyword tagging, such a peer-review system allows users to rapidly narrow down the links most applicable to their research need. Other features added provide link owners with the capacity to edit, manage and communicate on their own link without requiring input or support from the Bioinformatics Links Directory (8).

Although necessary to remain current and to advance the utility of the Bioinformatics Links Directory, these improvements will only prove useful if driven by the community. As a community-driven repository, everyone in the research or bioinformatics community has the opportunity to help make the collection better and more meaningful. Anyone may (i) suggest a link through links@bioinformatics.ca or through the ‘Suggest a URL’ page on the Bioinformatics Links Directory; (ii) register for a free account and submit their own tool or database; (iii) rate a tool, resource or database; (iv) register for a free account and submit their review of a tool, resource or database; (v) enrich a tool or database with tutorials or user-oriented content; (vi) initiate a discussion forum on a problem related to the use of any given tool or database or (vii) share a useful tool, resource or database with their colleagues. After a decade of output from the NAR Web Server issues, it will be interesting to monitor the development, maturity and impact of these bioinformatics web servers and databases over the next decade.

FUNDING

Ontario Institute for Cancer Research and the government of Ontario, and from Genome Canada and the Ontario Genome Institute though a platform award to the The Center of Applied Genomics (TCAG) at the Hospital for Sick Children (SickKids). Funding for open access charge: Waived by Oxford University Press.

Conflict of interest statement. None declared.

ACKNOWLEDGEMENTS

The Bioinformatics Links Directory is a community resource built on a commitment to the spirit of open access under the Attribution-Share Alike 2.5 Canada (CC BY-SA 2.5) license. The authors acknowledge the efforts of Nucleic Acids Research and the researchers and developers worldwide who invest considerable effort into ensuring that their research is freely accessible to all. In particular, the authors acknowledge all the contributors to the Bioinformatics Links Directory for their valuable input and suggestions for improvements to the directory; these individuals are listed on the Acknowledgements page at http://bioinformatics.ca/links_directory/acknowledgements/. In particular, they recognize the continued support of the OICR Web Development group, especially Joseph T. Yamada.

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