ATBI Model

All Taxa Biodiversity Inventory Model (András Gubányi, Imre Kilián, Veronika Kiss)

This page describes the modeling details of the EDIT project, with special focus on inventorying activities. After inteviewing some taxonomists from different field of taxonomy, modells of their inventory workflow and dataflow were created.

Inventory models describe the workflow of scientists from different fields of taxonomy. They show the chronological order of and the connection among different activities. A few activities are the same in case of different fields of taxonomy, but there are some activities, which occur only in selected fields, and there are also activities, which are unique, since they occur only in exceptional cases.


Operational functional model

for inventory activities:

Draft operational functional model

for inventory activities:

Activity diagrams and their semantics

UML activity diagrams consist of the following features:

  • Activities: (rounded boxes) describing certain activities. They may be primitive (steps) that cannot be broken up to parts, or they may be compound, that consists of a series of sub-activities. Compound activities are denoted by the infinite symbol (∞).

  • Activities may be extended by object tags. Special object tags are activity parameters. The direction of parameters can be determined by the direction of their incoming and outgoing object flow arcs.

  • Control flow arcs are arrows starting in one activity, and ending in another activity. Control flow arcs may attach guard conditions. If they exist, than the condition decides, if the prescribed change in activity is to be completed only if the guard condition evaluates to true.

  • Events are practically starting points of activities, which trigger certain chain or sub-network of the entire activity network.

  • Activity calls are compound activities that are detailed elsewhere. In general they act very similarly to subroutines or subprograms in traditional programming: they have a single definition that may be referred to elsewhere. They are denoted by a fork symbol (ψ).

  • Decisions, where, depending on the result of a condition, one of two or more outgoing arcs are activated. They are denoted by a rombus box (â—‡) with a notice, that describes the content of the decision.

Along the arcs of activity networks tokens are travelling. An activity has incoming and outgoing arcs, both of control flows and object flows. If arcs are active, we say, they have tokens. If all the incoming arcs are active, the activity is carried out. Having completed the actions of activities, tokens are multiplied, and are sent along the outgoing arcs of the activity.

Activities may contain other sub-activities that are carried out when entering the main activity. If a main activity has several arrows leading to sub-activities, then different threads are launched for all of the arrows. A main action is finished when all active threads (arcs coming from sub-activities, and arriving to the main activity) deliver their token.

Inventory Process

In the following we are giving the details of the workflow:

Preparation is the composite activity that comprises all sub activities, which are made still prior to fieldwork. They usually refer to management questions, and mostly managers execute them. The composite activity of Specification determines taxonomical groups, localities and methods, to be done in the preparation, management phase of the activities. Verification of specification in many cases means that based on literature data and previous experiences, the yield of methods can be previously estimated. The Human Resources activity covers practically the workflow of setting up a research team. It consists of several steps, and in end effect it results a personnel list.

Upon receiving a feasible specification, and the list of personnel, the research project can be design_ed. The final result of this stage is the research plan itself. _Verification of Design checks, if the proposed steps are feasible: i.e. they don’t exceed financial, material and time limits. The Expedition activity means the physical preparation of Fieldwork, i.e. managing the travel, estimation the money and labour capacity. Upon receiving the list of personnel and the research plan, actual steps can be started in the framework of Execution. These include (1) Fieldwork, i.e. doing research on the field (2) Lab work, i.e. collecting, organizing and publishing the results of fieldwork. Fieldwork is a generic concept that includes all the necessary phases and steps to be done in or near to the habitat. Fieldwork has four input parameters: 1. personnel list 2. research plan, where the research plan itself includes other important components, like permissions and the gazetteer database. All the working phases are included in the Lab work, which are completed in the laboratory, after arriving from fieldwork again. The input of this activity is the collection itself. The exact way how laboratory work is to be carried out, varies depending on the actual taxonomic group. Reporting is the last step of work after laboratory activities have been closed down. Reporting has three more or less independent phases: 1. writing the reports’ checklists, i.e. filling up some checklists, that were prepared still in the planning phase, but haven’t been filled in the reporting activities at the end of the field work. 2. inserting data into the inventory book 3. inserting data into collection database. The three sub activities must synchronize themselves before closing the reporting activity.


ATBI Interviews were made with the following researchers from the HNHM:

ATBI Interviews were made with the following researchers from the Staatliches Museum für Naturkunde Stuttgart:

ATBI Interview were made with the following researcher from the University of Erlangen-Nurenberg:

Interviews in connecting with Bottleneck Analisys were made with the following researchers from the Staatliches Museum für Naturkunde Stuttgart:

Presentations by the HNHM

London Meeting 2007 January:

Budapest Meeting 2007 May:

Inventory Model by HNHM

UML description

Updated by Andreas Müller about 1 year ago · 21 revisions