An ontology is a computable representation of the different parts of an organism and its different developmental stages as well as the relationships between them. The ontology of model organisms is therefore a fundamental tool for a multitude of bioinformatics and comparative analyses. The cephalochordate amphioxus is a marine animal representing the earliest diverging evolutionary lineage of chordates. Furthermore, its morphology, its anatomy and its genome can be considered as prototypes of the chordate phylum. For these reasons, amphioxus is a very important animal model for evolutionary developmental biology studies aimed at understanding the origin and diversification of vertebrates. Here, we have constructed an amphioxus ontology (AMPHX) which combines anatomical and developmental terms and includes the relationships between these terms. AMPHX will be used to annotate amphioxus gene expression patterns as well as phenotypes. We encourage the scientific community to adopt this amphioxus ontology and send recommendations for future updates and improvements.

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency–Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.

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BackgroundCiona robusta (Ciona intestinalis type A), a model organism for biological studies, belongs to ascidians, the main class of tunicates, which are the closest relatives to vertebrates. In Ciona, a project on the ontology of both development and anatomy has been developing for several years. Its goal is to standardize a resource relating each anatomical structure to developmental stages. Today, the ontology is codified up to the hatching larva stage. Here, we present its extension throughout the swimming larva stages and the metamorphosis, up to the juvenile stages.ResultsTo standardize the developmental ontology, we acquired different time-lapse movies, confocal microscope images, and histological serial section images for each developmental event from the hatching larva stage (17.5 h post-fertilization) to the juvenile stage (7 days post-fertilization). Combining these data, we defined 12 new distinct developmental stages (from Stage 26 to Stage 37), in addition to the previously defined 26 stages, referred to as embryonic development. The new stages were grouped into four Periods named: Adhesion, Tail Absorption, Body Axis Rotation, and Juvenile.In building the anatomical ontology, 204 anatomical entities were identified, defined according to the literature, and annotated, taking advantage of the high resolution and complementary information obtained from confocal microscopy and histology. The ontology describes the anatomical entities in hierarchical levels, from the cell level (cell lineage) to the tissue/organ level. Comparing the number of entities during development, we found two rounds of entity increase: In addition to the one occurring after fertilization, a second one occurred during the Body Axis Rotation Period, when juvenile structures appear. On the other hand, a high number of anatomical entities (related to the larva life) are significantly reduced at the beginning of metamorphosis. Data were finally integrated within the web-based resource “TunicAnatO”, which includes several anatomical images and a dictionary with synonyms.ConclusionsThis ontology will allow for the standardization of data underpinning an accurate annotation of gene expression and the comprehension of the mechanisms of differentiation. It will help create an understanding of the emergence of elaborated structures during both embryogenesis and metamorphosis, shedding light on tissue degeneration and differentiation occurring at metamorphosis.

NISEED (Network for In situ Expression and Embryological Data) is a generic infrastructure for the creation, maintenance and integration of molecular and anatomical information on model organisms. We applied it to ascidians which are marine invertebrate chordates. These animals constitute model organisms of choice for developmental biology because their embryos develop with a small number of cells and an invariant lineage, allowing their study with a cellular level of resolution. In ANISEED (Ascidian NISEED), embryogenesis of ascidian is represented at the level of the genome via functional gene annotations, cis-regulatory elements or gene expression data, at the level of the cell by representing its morphology, fates, lineage, and relations with its neighbors, or at the level of the whole embryo by representing its anatomy and morphogenesis at successive developmental stages. The system provides also tool and standard to enter, annotate, curate and manage data. All results can be accessed through the ANISEED website at "http://aniseed-ibdm.univ-mrs.fr":http://aniseed-ibdm.univ-mrs.fr