A number of terms related to identification tools are introduced
and the advantages of selected types of identification keys are compared

Hagedorn, Gregor

Martellos, Stefano

Rambold, Gerhard

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59Types of identification keysGregor Hagedorn, Gerhard Rambold, Stefano MartellosAbstract — A number of terms related to identification tools are introduced and the advantages of selected types of identification keys are compared.Index Terms — Identification tools, single-access key, dichotomous key, polytomous key, lead, couplet, free-access key, multi-access key, matrix key, multi-entry key.——————————  u  ——————————1 introductionThe generalization of individuals (things, events, etc.) into classes is essen-tial to transfer knowledge across individual incidents. When learn ing a language, we learn the defining features of classes like “table”, “chair”, “shrub”, etc. Similarly, biology defines formal classes for living things (called “taxa”) together with class names (“taxon names”) and defining descriptions. The assignment of an unknown object to a taxon is called “identification” or “determination”. To non-biologists this may be confusing, the term “identification” being more commonly associ ated with the naming of individuals (as in “ID card” or “record identifier”).The number of taxa in biology is very large. For example, currently about 900 000 insect taxa alone are recognized. Compared to the aver age vocabulary of an educated English native speaker of roughly 25 000 words, it is clear that teaching the vast “taxon vocabulary” to biology students was always problematic. Although comparing a collected spe cimen sequentially with published descriptions or re presentative speci mens is an essential identifica-tion method, any “linear search” method comparing one specimen after another soon becomes impractical.Biologists have therefore developed various forms of “identification keys” to “unlock” the knowledge that would otherwise remain inaccessible. These are essentially “divide and conquer” search algorithms that re duce the result set recursively until the remainder is small enough to be sol ved by direct comparison. The fastest algorithms are those that pro vide a division into equally sized partitions (leading to search algorithms that scale logarithmically with ————————————————G. Hagedorn is with the Julius Kühn-Institute, Federal Research Centre for Cultivated Plants, Institute for Epidemiology and Pathogen Diagnostics, Königin-Luise-Straße 19, D-14195 Berlin, E-mail: gregor.hagedorn@jki.bund.de. – G. Rambold is with the Department of Mycology, University of Bay reuth, D-95440 Bayreuth – S. Martellos is with the Dept. of Life Sciences, Univ. of Trieste, I-34127, Trieste, Italy. E-mail:martelst@units.it.Nimis P. L., Vignes Lebbe R. (eds.) Tools for Identifying Biodiversity: Progress and Problems – pp. 59-64.ISBN 978-88-8303-295-0. EUT, 2010.60the number of taxa). Biological keys don’t al ways provide this, because other factors (character observation reliability, convenience, cost, etc) conflict with the desire to provide fastest progress. The authors of biological identification keys, however, typically realize that evenly splitting choices are desirable.2 Single-acceSS, multi- or free-acceSS, and multi-entry keySThe most traditional biological identification keys are the easily printable dichoto mous (every choice has two alternatives) or polytomous (two or more options at each choice) forms. The structure of these keys typically consists of a series of alternative statements, called “leads”. All leads that need to be evaluated for a single decision form a “couplet”.Clearly, dichotomous keys are a special case of polytomous keys. For simple choices involving a single characteristic (a “character” or “feature”), such as “wings: 1. present 2. absent” or “flower colour: 1. red 2. blue 3. pink 4. yellow”, the number of options matters little. However, to achieve reliable identification in the face of natural variability and continuous varia tion, it may be desirable to use complex Boolean statements involving multiple characters. For example, “leaves hairy and flowers red” versus “leaves glabrous or flowers not red” may be used in a case where the alternative may include glabrous plants with pinkish-red flow ers, or plants with mixed hairiness but other flower colours. Although it is theo re tically possible to construct a polytomous key with Boolean lead statements, practice has shown that the result is often akin to a logical riddle. Many editors therefore recommend or require the use of di cho tomous keys.However, a key may be a mixture of simple polytomous and complex di-chotomous choices. The generalizing term “single-access key” [1] is there fore used in the present paper to include both dichotomous and poly to mous keys. The equivalent term in computer science is “decision tree”.Question 2Question 3 ...Question 1Question 4Question 5Question 6Question 7..........Question 5Question 1Question 2Question 3Question 4Question 5Question 1Question 2Question 3Question 4Question 5...Question 4Question 3Question 2Question 1Fig. 1 – User interaction steps in a single-access key (left, the sequence of steps follow the data structure) and a free-access key (right, the sequence is determined by the user). From [2].An alternative to a single-access key is the free-access key (also known as multi-access key, matrix key, or, incorrectly, “synoptic key”1). Whereas in a single-access key a fixed sequence of choices (decisions) is defined by the author (providing a single path to each result), in a free-access key the sequence of choices is up to the user. In every step, the user can se lect from the list of characters offered, and choose a matching state or value. Thus a free-access key is the set of all possible single-access keys that arise by permutating the order of characters (Fig. 1). Al though print able free-access keys exist, they ————————————————1 The term „synoptic key“ has traditionally been used for single-access keys that reflect the taxonomic hierarchy. Its use for multi-access keys (especially printable ones) should be avoided.61are most suitable for computer-aided identification tools, and have a long de-velopment history [3]. Examples are DELTA-IntKey [4], Lucid [5], NaviKey [6], Xper2 [7]. The Flash-based IBIS-ID [8] was newly developed in KeyToNature.In a free-access key, the choice of characters is repeated at every step. A related form, the multi-entry key, allows free choice of characters in a first step (a “multi-character-query-form”), followed either by a field-guide-like listing of remaining taxa, or by a dynamically generated (filtered) single-access key (as in the FRIDA/Dryades keys [9]).Single-Access Free-Access Multi-EntryInformation  reductionHighNone (complete informa-tion is opti mal)Variable (none if all characters are avail able in the initial step)Average identification  speedDepends on the creators of the keyDe pends on user’s back-ground knowledge; may ex ceed averageVariable between single and multi-accessComplex  statements  (and, or, etc.)Yes (not recommen ded for poly tomous keys)No“No” in entry-form, “yes” in following single-access keyQuestion- answer stylePossible for simple statements(Implicit in char acter state or value choice)(Implicit in charac-ter state or value choice)Difficulty of  choosing next  decisionNone Often high for beginnersVariable; depen ds on completeness of initial entry formSkipping un-answerable choicesDifficult; all alternative paths must be follow ed to the endEasyEasy in entry-form, difficult in an optional single-access partResources required for  constructionLow for first draft. Good keys require high expertiseHigh investment until first version can be testedHigh for data matrix, but the size of the matrix is variableTab. 1 – Comparison of some identification methods. The comparison is aimed at manually created single-access keys (those generated from a data matrix are not considered here).An evenly splitting single-access key requires fewer decisions from be ginners than a multi-access key. The latter may in fact generate faster progress in terms of “steps”, but requires additional decisions as to which character to use next. Even if the character list is ordered by character suit ability and fastest progress, beginners will be tempted to use execute their free character choice. This is problematic if many characters are not yet understood. In contrast, the fixed 62identification path of a single-access key also fixes which terms and concepts must be learned first. A disad van tage of single-access keys is that identification may be impossi ble if a choice cannot be decided at all. This may occur because a charac ter can not be observed (e. g., a developmental stage is not present in the spe ci men), or because the options are not communicated clearly enough. The resulting frustration can be high, especially for beginners.Both free-access and multi-entry keys truly excel in their performance when used by experts. For these, character selection is intuitive and fast. By choosing characters, for which a rare state is present in the specimen, identification progress can then be on an order of magnitude faster than using a single-access key. This is already possible with moderate experi ence, since states that were never observed by a user before are, by defi ni tion, rare. Tab. 1 gives an overview of some differentiating features.From an author’s perspective, matrix-based keys require a high initial in vest-ment to research and fill a large character × taxon matrix. In con trast, single-access keys require less formal investment. Due to the inher ent information reduction (most characters apply only to a rela tively small sub set of taxa), a reviewable key is faster to produce and proof-reading is less time-consuming than the creation of an equivalent data matrix con tain ing all characters for the same group of taxa. However, a success ful single-access key depends strongly on the expertise of the author to chose characters that are convenient, cost-effective, reliable across all taxa in the subtree, and avail able throughout a large period of the de vel op mental cycle of the organ ism. Single-access keys may therefore require several cycles of testing until initially overlooked problems have been fixed; their production can be akin to the “debugging” of software code.Furthermore, the creation of matrix-based keys generally requires learn ing a special-purpose application like DELTA or Lucid, whereas single-access keys may be created in a text-processing application. There fore, although newly created single-access keys may occasion ally be problematic to use, they offer con siderable benefits to both pro du cers and consum ers. Single-access keys, until re cent ly, have been developed only rarely as com-puter-aided, interactive tools. Notewor thy developments in this direc tion are the commercial Lucid Phoenix applica tion [10], the FRIDA/Dry a des software [9], [11], the KeyToNature Open Key Editor” [12], and the open source WikiKeys and jKey [13] application on biowikifarm [14].3 Structural variantS of Single-acceSS keySTwo additional structural variants of single access keys are relevant when building information models [2]: 1. Couplets may consist of a ques tion, with the leads providing contrasting answers. This question-answer-style is of ten appealing to beginners. However, complex statements (involving more than one character and Boolean expressions) are not possible. Where as a mixture of simple polytomous and complex dicho to mous couplets in a single key is quite intelligible, a mixture of simple quest ion-answer-style with question-less complex dichotomous couplets is not. 2. The desire for fast identification progress using 63conven ient char ac ters often conflicts with character variability in a subset of organisms. As long as the character is reliable for the majority of taxa, a frequent solution to this problem is to key out taxa with variable character expression multi ple times. This may affect only the terminal taxa, or entire branches of the keys. Whereas the first case will often simply be handled by true duplica tion, multiple references to entire branches of a decision tree turn a “tree” structure into a directed (and generally acyclic) graph (DAG) and requires careful attention when modelling information models or software. In biol ogy a DAG is sometimes called a “reticulated” identifica tion key.Linked Key Style (also called “parallel”, “juxtaposition” or “bracketed” style):1. Ovule solitary, basal ..........................................................................................................2– Ovules numerous, axile or free-central .............................................................................32. Perianth green, membranous or absent; filaments free .........................Chenopodiaceae– Perianth translucent and papery; filaments often united below  ...............Amaranthaceae3. Placentation axile; leaves alternate  ............................................................Saxifragaceae– Placentation basal or free-central; leaves usually opposite ............................................. 4Nested Key Style (also called “yoked” or “indented” style):1. Ovule solitary, basal2. Perianth green, membranous or absent; filaments free .....................Chenopodiaceae2. Perianth translucent and papery; filaments often united below ...........Amaranthaceae1. Ovules numerous, axile or free-central3. Placentation axile; leaves alternate  ........................................................Saxifragaceae3. Placentation basal or free-central; leaves usually oppositeFig. 2 – Examples of the linked and nested styles of branching keys in lead style; see [2] for derivation.4 preSentational variantS of Single-acceSS keySThe dominant presentation styles of single-access keys are shown in Fig. 2. In “linked” keys the connection between couplets is achieved by a link ing reference (at the right side) to a couplet ID (left). In nested keys direct nesting of couplets replaces the explicit linking. Nested keys are more commonly known as “in den-ted”, but unfortunately this refers to an acci den tal (albeit fre quent) rather than essential quality [3]. Nested keys may be printed without indentation to preserve space (relying solely on corres pon ding lead symbols) and linked keys may be indented to en hance the visibility of the couplet structure. Further presentational (“solid keys”, “graphical style”) and semantic (“arti ficial” or “diagnostic” versus “natural”, “synoptic”, or “phylogenetic”) variants exist; see [2].5 SummaryThe order of couplets (choices) in an identification tool may be defined by the creator (single-access key), or may be freely selectable by the user (free-access key). A multi-entry key is an intermediate form that may com bine advantages of both forms if only a small character subset is included in the multi-entry phase. 64Structural criteria for single-access keys are: a) whether the leads in a couplet are limited to two (dichotomous) or not (polytomous key); b) whether couplets are limited to a single character or combinations of multiple characters, involving Boolean operators such as ‘and’, ‘or’, or ‘not’, are supported; c) whether taxa may be keyed out in mul tiple places, and whether redirections into entire sections (or “bran ches”) of the key are supported (“reticulated key”); and d) whether leads in couplets are complete statements or split into a question with the couplet and leads providing the answers. Certain presentational forms (nested key versus linked keys) are not structurally relevant.acknowledgementThis work was supported by the KeyToNature Project, ECP-2006-EDU-410019, in the eContentplus Programme. We thank P. L. Nimis and B. Press for review and important suggestions.referenceS[1] J. Winston, Describing Species. Columbia University Press, 1999.[2] G. Hagedorn, Structuring Descriptive Data of Organisms — Requirement Analysis and Information Models. Ph. D. Thesis, Universität Bayreuth, 2007.[3] R. J. Pankhurst, Practical Taxonomic Computing, 1991.[4] DELTA – DEscription Language for TAxonomy http://delta-intkey.com/, 2010-07.[5] Lucidcentral.org http://www.lucidcentral.com, 2010-07.[6] D. Neubacher and G. Rambold, NaviKey – a Java applet and application for access ing descriptive data coded in DELTA format, 2005 (onwards). http://www.navikey.net, 2010-07.[7] V. Ung, G. Dubus, R. Zaragüeta-Bagils and R. Vignes Lebbe, “Xper2: introducing e-taxonomy”. Bioinformatics, 26 (5): 703-704, 2010; doi: 10.1093/ bioinformatics/btp715; see also http://lis-upmc.snv.jussieu.fr/lis/?q=en/resources/software/xper2.[8] M. Giurgiu, G. Hagedorn and A. Homodi, “IBIS-ID, an Adobe FLEX based identification tool for SDD-encoded multi-access keys”. Proc. of TDWG 2009, 9-13 Nov. 2009, Montpellier, p. 90, 2009.[9] S. Martellos and P. L. Nimis, “KeyToNature: Teaching and Learning Biodiversity. Dryades, the Italian Experience”. In: M. Muñoz, I. Jelìnek, F. Ferreira (eds.), Proceedings of the IASK Interna tional Conference Teaching and Learning 2008, pp. 863-868, 2008.[10] Lucid Phoenix (http://www.lucidcentral.org/LinkClick.aspx?link=152), (2010-07).[11] S. Martellos, “Multi-authored interactive identification keys: The FRIDA (FRiendly IDentificAtion) package”, Taxon, vol. 59 (3), pp. 922-929, 2010.[12] S. Martellos, E. v. Spronsen, D. Seijts, N. Torrescasana Aloy, P. Schalk and P. L. Nimis, “User-generated content in the digital identification of organisms: the KeyToNature approach”, Int. J. Information and Operations Management Education, vol. 3, 3, pp. 272-83, 2010.[13] S. Opitz, G. Hagedorn, “The jKey wiki key player and builder”. Proc. of TDWG 2009, 9-13 Nov. 2009, Montpellier, 2009.[14] G. Hagedorn, G. Weber, A. Plank, M. Giurgiu, A. Homodi, C. Veja, G. Schmidt, P. Mihnev, M. Roujinov, D. Triebel, R. A. Morris, B. Zelazny, E. van Spronsen, P. Schalk, C. Kittl, R. Brandner, S. Martellos and P. L. Nimis, “An online authoring and publishing platform for field guides and identifi cation tools”. In: P. L. Nimis and R. Vignes Lebbe (eds.), Tools for Identifying Biodiversity: Progress and Problems, pp. 13-18, 2010.

Types of identification keys

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Types of identification keys

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