Existing data sources Image databases

There are huge numbers of online databases specifically in the biodiversity field (Parker, 2010). Some of these databases provide image database as one of the system functions. After going through these image databases, most of databases provide almost the same system requirements and features but they are used in different domains such as catfish, ants, insects, birds and plant. Thus in this study, only five were selected for reviewing purposes.

a) FlyBase (http://flybase.org/)

FlyBase (McQuilton et al., 2012) is an image database of Drosophila genes and genomes. One of the query tools provided in this system is ImageBrowse (see Figure 2.1) for browsing the images based on the organ system, life-cycle stages, major tagma, germ layer and all species images.

The images in this database were collected from the literatures such as journal articles and books. The retrieved images are listed in unranked order along with a short description (see Figure 2.2).

Figure 2.2: Retrival results from FlyBase

b) Global Cestode Database (GCD) (http://tapewormdb.uconn.edu/)

The Global Cestode Database – GCD initiative was funded by the U.S. National Science Foundation’s Partnership for Enhancing Expertise in Taxonomy Program (PEET). The project began in 1995 at the University of Connecticut in Storrs, but has developed into an ongoing collaboration among Cestodologists in nine countries from around the world (Caira, 1995). The GCD provides a resource about the global cestode or tapeworms, whereby it has currently progressed on the entry of taxonomic names and literature. For easier accessing and tracking of the database elements, they have migrated from multiple FileMaker Pro databases to a single MySQL database. It allows direct data entry and uploading of PDFs from any site in the world that has Internet access.

As shown in Figure 2.3, the information can be searched based on the four main categories, which are Cestode Scientific Name, Type Host, Type Locality and Specimen. For image retrieval, there are a few parameters given and users have to select the category based on their interest. Any images that are related to taxonomic classification as shown in Figure 2.4 will be retrieved together as shown in Figure 2.5.

Figure 2.4: Retrieved results from GCD

Figure 2.5: Retrieved images from GCD

c) Specimen Image Database – SID (http://sid.zoology.gla.ac.uk/)

Specimen Image Database – SID (Simon & Vince, 2011) is a searchable database of high-resolution images for phylogenetic and biodiversity research. This database is

intended as a reference collection of named specimens and a resource for comparative morphological research. Each image is accompanied by a fully searchable annotation, and can be browsed, searched or downloaded. Public users can register in this database and the registered users can add, annotate or label the images. Currently, this database is devoted to the insect order Phthiraptera (lice) and contains 7650 images of 440 taxa.

Key features of SID (see Figure 2.6) include web upload/download of images, bulk and single image annotation via web forms, extensive browse and search options by text query, web service facility, web utility to label specific image features, taxonomy served and validated independently by the Glasgow Taxonomy Name Server, plus alias addresses for images by accession number and freeware which allows anyone to set up the database and serve their own images. The retrieved images are listed in unranked order with the taxon information, host as well as image properties.

d) Universal Chalcidoidea Database (UCD) (http://www.nhm.ac.uk/chalcidoids)

The Universal Chalcidoidea Database – UCD currently contains citations of taxonomic names made available within the Chalcidoidea. It includes a comprehensive list of the various generic combinations and misspellings that have been used in the literature. Also included are host/associate and distribution records, for which the latter can be used to provide regional lists of Chalcidoidea (Noyes).

Figure 2.7 shows the searching page in this database. A bibliographic database lists over 40,000 references have been used in Chalcidoidea and this can be searched using 120 predefined keywords in order to locate references dealing with specified subjects. A similar search can also be conducted in the taxonomic part of the database. More than 350 images of a wide range of living chalcidoids are also available. The full set can be browsed or restricted to images specific to a particular family, genus or species. A new aspect of this database is the inclusion of .pdf files of references. Currently, it is limited to papers by Girault (by permission of Michael Schauff) and Grandi (by permission of Jean-Yves Rasplus). A .pdf icon alongside the reference in the bibliographic database indicates the presence of these .pdf files.

Figure 2.7: Universal Chalcidoidea Database – Search page interface

The images can be retrieved by using text query based on the taxon family, or by browsing the entire image database as shown in Figure 2.8. The retrieved images are listed in unranked order with the taxonomic classification and additional information such as the owner of the photo and image description.

e) MonoDb (http://www.monodb.org/index.php)

MonoDb (Andy & James, 2012) is another biodiversity database that provides image gallery as one of the features in the database. MonoDb is a web-host for the parasite monogenea. As mentioned in this website, the purpose of this website is to help children, adults, experts and non-experts to learn more about this fascinating group of animals. Browsing the entire images provided in the database can retrieve images in this database. The images are listed randomly and no information is attached to the images (see Figure 2.9).

Figure 2.9: Monogenean images in MonoDb