Ecoinformatics

A few definitions have been circulating, mostly centered on the creation of tools to access and analyze natural system data. However, the scope and aims of ecoinformatics are certainly broader than the development of metadata standards to be used in documenting datasets. Ecoinformatics aims to facilitate environmental research and management by developing ways to access, integrate databases of environmental information, and develop new algorithms enabling different environmental datasets to be combined to test ecological hypotheses. Ecoinformatics is related to the concept of ecosystem services.

Ecoinformatics characterize the semantics of natural system knowledge. For this reason, much of today's ecoinformatics research relates to the branch of computer science known as knowledge representation, and active ecoinformatics projects are developing links to activities such as the Semantic Web.

Current initiatives to effectively manage, share, and reuse ecological data are indicative of the increasing importance of fields like ecoinformatics to develop the foundations for effectively managing ecological information. Examples of these initiatives are National Science Foundation Datanet projects, DataONE, Data Conservancy, and Artificial Intelligence for Environment & Sustainability.

Software Development Lifecycle

Central to the concept of ecoinformatics is the Software Development Lifecycle (SDLC), a systematic framework for writing, implementing, and maintaining software products. Typically in Ecoinformatics projects, the development pipeline includes data collection, usually from several different environmental data sources, then integrating these data sources together, and then analyzing the data. Here, each step of the SDLC is described in the context of ecoinformatics, per Michener et al. It is important to note that the plan, collect, assure, describes and preserve steps refer to the data collection entity, which can be individual researchers or large data-collection networks, while the discover, integrate, and analyze steps typically refer to the individual researcher.

Plan: Ecoinformatics projects require data from several databases. Each database holds different data, and therefore researchers should identify what types of environmental or ecological data they will need to answer their research question.

Collect: Data is collected in several different ways. In ecoinformatics, this is usually restricted to manually entering data into a spreadsheet, and parsing data from an existing database. The growth of relational databases has made it easier for ecologists to download relevant data and integrate datasets together

Assure: Data entries should be checked thoroughly to validate their accuracy and usability, such as to check for outliers and erroneous points. The same principle applies to data downloaded from datasets. This responsibility falls on both the ecologist downloading the data, and the entity that sets up the data collection system.

Describe: An accurate description of the metadata of a dataset that is used in a study should include enough information to deduce the data collection and processing methodology, when the data were collected, why the data were collected, and how the data were stored. This is important for reproducibility, especially for projects that build on each other and may recycle data

Preserve: After data is collected by an institutional entity, it should be archived such that it is easily accessible. Ideally, this is in databases that are maintained and not at risk of deprecation

Discover: While there are good practices for discovering data to start a research project, this process is often marred by a lack of usable, published data, as researchers may collect data specific to their study, but may not publish this data for wider use. On the data collection end, this can be addressed by better data-sharing practices, such as by linking datasets when publishing papers or studies. On the data procurement end, this can be addressed by more precise data searching, such as using key words to find relevant datasets.

Integrate: Synthesizing datasets together can be difficult and labor-intensive, largely due to the methodological differences in data collection. There are several approaches to this, but the best practices typically involve computational approaches, namely using R or Python, to automate the processes and prevent errors

Analyze: Data analysis can take several forms, and should be tailored to the specific ecological project. However, all data analysis methods should be well-documented, including the procedure for analysis, justification for analysis methods, and any shortcomings in a specific approach.