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The synonyms of biological species names are shown to be an important component in comprehensive searches of electronic scientific literature databases but they are not well leveraged within the major literature databases examined. For accepted or valid species names in the Integrated Taxonomic Information System (ITIS) which have synonyms in the system, and which are found in citations within PLoS, PMC, PubMed or Scopus, both the percentage of species for which citations will not be found if synonyms are not used, and the percentage increase in number of citations found by including synonyms are very often substantial. However, there is no correlation between the number of synonyms per species and the magnitude of the effect. Further, the number of citations found does not generally increase proportionally to the number of synonyms available. Users looking for literature on specific species across all of the resources investigated here are often missing large numbers of citations if they are not manually augmenting their searches with synonyms. Of course, missing citations can have serious consequences by effectively hiding critical information. Literature searches should include synonym relationships and a new web service in ITIS, with examples of how to apply it to this issue, was developed as a result of this study, and is here announced, to aide in this.

Latin binomials, the scientific names of biological species, are typically used as terms in searches for literature across the biological disciplines. However, because synonyms for those binomials often exist, the efficiency of individual binomials in guaranteeing retrieval of all relevant items can be greatly affected by the inclusion (or exclusion) of synonyms in the search. In biological nomenclature, synonyms are scientific names, other than the currently accepted one, that apply to an organism. The purpose of this study is to assess the importance of this effect in online searches of a popular cross-section of relevant scientific literature databases.

Important Synonyms Pdf Download

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In this paper, I provide a repeatable and quantifiable snapshot of the effect of synonyms on searches in a very large commercial scientific literature index, Scopus [1], two related public indexes, PubMed [2] and PubMed Central [3] and the smaller but broader Public Library of Science (PLoS)[4]. Search queries were all generated and conducted using only online interfaces. The general idea was simply to search every accepted or valid species in the Integrated Taxonomic Information System ITIS [5] that had at least one synonym, against each of the aforementioned online databases and then run each of those searches again including all synonyms for each species, thus allowing a direct assessment of the effect of synonyms in the number of citations retrieved. Binomials were chosen as the units of comparison because of their unique combination of a specific rank (species) with a unique lexical structure consisting, in canonical form, of an ordered string of two paired tokens, the genus and specific epithet. This allows a much higher degree of comparability in results than one would get with the inclusion of monomials, while still retaining a much larger sample than would be gotten with trinomials alone. Trinomials, also suffer from a high level of variance in their presentation in the literature with respect to whether or not a rank indicator is employed in the string, what the abbreviation for that indicator is, and when not present, in the rank itself.

Hopefully, this work will serve as a baseline for later studies looking at the same issues as this one but in hindsight after efforts have been made to address the problem, as well as an indication of the importance of synonyms in online searches.

Two species, Anodonta anatina and A. cygnea, had 303 and 285 synonyms respectively. Individual sets were generated for each of those species to query them separately for each source by individual synonym to investigate the contributions of individual synonyms and because their ensemble Boolean synonym strings exceeded the query string length limit for all sources. Due to differences in what individual services would accept, such as maximum query string length and different special characters, there was some variance in the actual number of names successfully queried per source. This amounted to less than 0.1% of names. However, a base set of 67,187 accepted or valid species names and their 139,207 synonyms were successfully queried for every source.

Among all valid or accepted species names in ITIS, only those with synonyms (~17%) were used in this study, and among those, the number yielding any citations at all varied widely across kingdoms and sources. See supporting documentation. However, for those species that had synonyms, and citations in the literature, both the number of species affected by adding synonyms to the search string (See Table 1), and the number of citations returned (See Table 2), was generally substantial.

In Scopus there are rarely synonyms in a keyword field, and in PubMed and PMC this is also the case. PubMed and PMC also have an added redirection in search to use MeSH terms when a species is not found among the citations but found in MeSH. This is also a rare and serendipitous case because MeSH does not maintain species level synonymy. In runs of all species against both resources querying only the abstracts in the case of Scopus and the title and abstract in the case of PubMed, of course the raw numbers of citations returned were greatly diminished. In PubMed the percentage of species for which citations were found and synonyms made a difference in the number of citations returned remained within 1% of the values obtained for the full record search in all kingdoms. In Scopus, there was wider variance with a reduction of up to 14% (in the case of Animalia) but an increase of 4.7% Chromista. Further heuristic investigation of the Scopus data suggested that the effect was primarily due to Scopus having richer records in many cases with full titles of articles in the references (and thus having searchable species names in those titles) and with species names in the full text of the many articles in Scopus that have it, not just the abstract.

The value of synonyms in general, especially those in common use at one time, is clear. At the individual species level, a given source in this study may or may not have had citations for the accepted name of a species or its synonyms, but across all sources and kingdoms, there was always at least a minimal effect of adding synonyms to the search. And sometimes, such as in Archaea, nearly all searches for names that had synonyms were incomplete without those synonyms. Strangely with the NCBI databases, there is actually a limited set of synonymy available within the separate NCBI taxonomy database, but it is not automatically integrated into their general search like MeSH is. One could use it separately and transfer the results manually, or build a service to use it in an integrated way, but I found none available at this point. The bottom line is that users looking for literature on specific species across all of the resources investigated here are often missing large numbers of citations if they are not manually augmenting their searches with synonyms. This can have serious consequences. The range of a species known by different names in different regional treatments will erroneously appear restricted. A physician treating a pathogen known more commonly by another name will be blind to the bulk of potentially life-saving literature.

Stemming directly from the results obtained from the preliminary work associated with this study, ITIS has implemented within a high speed Solr web service [9], the ability to retrieve a list of synonyms for the accepted or valid name, associated with any synonym, as well as for the accepted or valid names themselves. Output is available in JSON, JSONP, Serialized PHP or XML. This allows their efficient use in dynamic search string expansion for virtually any web application, or as a way to add synonyms to any existing database. A simple example application which takes a user entered species name and constructs an appropriately formatted search string of the accepted or valid name of the species along with all of its synonyms (as used in this study) and then sends that to the chosen resource for query is provided on the ITIS website [12]. The application also exploits this capability for commercial search engines which no longer allow the kind of large scale automated interrogation used in this study (Google, Google Scholar and Bing). Any user trying one of these examples will see that the conclusions reached here also currently extend very similarly to those resources as well. 006ab0faaa