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Macrobenthic analysis was the first type of sample analysis data supported by ABACUS. Since it's first usage in 2018, macrobenthic analysis features have been continually improved and now possesses a range of features and processes that help to reduce the time taken to record macrobenthic data, improve the quality of the data and provide the tools and features to perform effective data management. All of this is backed up by its usage in real-world projects since 2018.

Clients using ABACUS for macrobenthic analysis have reported a reduction of 20% staff time in the data entry tasks alone. Combining this with substantially improved data quality, management, reporting and single-click exports, means laboratories are able to reduce the cost of processing macrobenthic samples, and get higher quality data available for release sooner.

Added to ABACUS in 2021, the Internal QC (Quality Check) report acts as a tool to provide internal feedback on the effectiveness and accuracy of staff involved in the extraction and identification of taxa during macrobenthic analyses. This can be used to identify training requirements for staff or alert to potential risk areas in projects that may require further quality checking.

ABACUS - Automatic Aphia record retrieval during taxonomic identification
Automatic Aphia record retrieval during taxonomic identification

Latest species names and data automatically retrieved from external sources

Integrated WoRMS link

ABACUS has integrated the published WoRMS APIs into its taxonomic identification process to allow users to automatically retrieve the latest information from WoRMS including the most up to date species names and taxonomic classification data (and with more data retrieved coming in a future update). Users can be sure that the data they are recording is based on the most up to date information available and is available with no extra effort.

ABACUS Copy Taxa video on Vimeo
Demonstration of the Copy Taxonomic Identifications feature within ABACUS. This feature lets you copy taxonomic data from another sample in the same survey and is useful when you are identifying several of the same species in many samples within a survey. This saves time and improves accuracy during data collection.

Taxa Identifications can be copied in bulk from an existing sample

Copy Taxa

When samples in a survey have the same species occurring many times the process of adding those records can become repetitive for staff. To solve this, ABACUS offers the ability to copy all the taxonomic identification data from an existing sample in the survey.

Taxonomic data is copied with the same identification data (name, Aphia ID, qualifiers, etc.) but the abundance is reset to zero. Users are then able to quickly edit the counts using the '+' and '-' buttons or edit the full record to make other changes.

Data quality checks are performed throughout ABACUS and a warning is shown whenever identifications are found with a zero count abundance, prompting staff to remove a copied taxa if it is not actually present in the sample.

Click the video to view the Copy Observations process in action

Taxa Identifications can be imported in bulk using the ABACUS import module

Import Taxa

When survey data already exists outside of ABACUS or a laboratory prefers a 'fieldwork' approach to collecting information (with users initially recording data in files separate to ABACUS), the ABACUS Import Module can be used to import taxonomic identification data in bulk.

The provided Excel-based template is fully documented and allows taxonomic identification to be imported in a taxa matrix format, so it can be used to import both historic datasets and where a 'fieldwork' approach is used. 

Data quality checks are performed automatically as part of the import process guaranteeing that only high quality makes it into ABACUS.

Record changes and corrections to identifications with full auditing and accountability

Quality Checks

A dedicated quality check stage in the taxonomic identification process allows changes to be made in a controlled and auditable manner (typically performed by a more senior taxonomist).

Identifications can either be removed, amended or new identifications added. Each type of change is recorded separately to the original data ensuring that a full history of each identification is available.

Details of the changes made are a valuable learning tool for users as well as offering a structured and controlled method to perform quality checks on your data.

Comprehensive statistical reports of extraction and identification efficiency

Internal QC Report

Probably deserving of a dedicated Showcase section of it's own, the ABACUS Internal QC report was included in an update in 2021.

Based on common methods used to perform external audits/QC (between two separate laboratories), the Internal QC report is generated by comparing results after Identification and Identification QC tasks. The report provides detailed statistical measures to monitor extraction and identification performance within your samples.

Reports include Estimation Of Taxa (rate of correct taxonomic identification), Number Of Individuals (proportion of specimens successful extracted from sample) and the Bray Curtis Similarity Index (similarity of results between Identification and Identification QC).

Export taxonomic data in matrix and list format with no manual interaction

Export Taxa

The ABACUS Export Module allows export of data in the common MEDIN template (and is confirmed as MEDIN compliant).

The produced exports include both Taxa Matrix and Taxa List formats, providing both options to your statisticians or clients without any further, error prone, manual transformation required.

Combined with ABACUS' use of controlled vocabulary lists and data quality reports that run alongside data exports, you will have the tools to improve speed and quality of data management during your exporting and reporting processes.