AMIS, The Article Minimum Information Standard

The curation process is significantly slowed down by missing information in the articles analyzed (for example, the identity of the clones used to generate ISH probes, the precise sequences tested in reporter assays, etc..). To help authors ensure in the future that necessary information is present in their article, we defined the Article Minimum Information Standard (AMIS) guidelines. This standard describes for each experiment the mandatory information that should be mentioned in literature articles to facilitate the curation process. These guidelines extend the minimal information defined by the MISFISHIE format (Deutsch at al. 2008, _Nature Biotechnology_). This standard was deduced from the ANISEED curation pipeline (Tassy, Dauga, Daian, Sobral et al. 2010, _Genome Research_). ANISEED is a generic infrastructure for the creation, maintenance and integration of molecular and anatomical information on ascidians. Thanks to the ANISEED curation pipeline, the capture of published information was streamlined by the creation of the “Article Card” concept. Each Article Card summarizes in a standardized and structured format the content of the text and figures of an article. It lists, and links to the corresponding experimental evidences, all features studied (genes, cell fates, etc...). This curation strategy allowed pointing out missing information essential to transform the “biological interpretability” of the data into their “computability”. AMIS was defined to obviate this problem. The MISFISHIE format doesn’t include the minimal information necessary to describe cis-regulatory elements. In ANISEED, a sophisticated representation of the structure of cis-regulatory elements and their upstream regulators was designed. AMIS details the minimal information to describe a regulatory region. To facilitate regulatory region data transfer between databases, a document type definition (DTD) was developed, following the AMIS rules