In parallel to the further development of the Aniseed system, a major issue is to optimise data collection. For this, your input is crucial.

For example, a large fraction of experimental data collected in your lab will probably remain unpublished. These data, which may not be very interesting to you, could however be of crucial interest for someone else in the community, and vice versa. Also, entering data into Aniseed is a great way to back up high-resolution data including images, to organize data, to compare data with those obtained by other groups. And your data can stay private if you wish, so that no one else can see them. Not even our curator team.

Entering published literature is also critical, for the system, and for the visibility of the papers. You have probably already been in the situation in which you remember that someone carried out a crucial experiment for your project. But where was it? Who did it? What was precise result obtained? Scanning Pubmed will not give you the answer if it is not in the article's abstract but a simple interrogation of Aniseed will return what you are looking for. That is, provided the paper has been entered in the database. Conversely, any paper entered into Aniseed has an increased impact because it pops up when looking for regulators of a given gene, or genes involved in a process, or lineage tracing experiments, etc. Even if the result is mentioned in the main text, but not the abstract. Even if it is in a supplemental figure!

• Expression patterns during normal development as well as in response to experimental manipulation (embryological or molecular)
• Morphological phenotypes
• Cis-regulatory element informations (gene reporter activity, binding sites, etc.)
• Molecular tools (inhibitors, constructs, morpholinos, etc.)

Unpublished data can be entered independently of one another.
For published data, you need to adopt a more rigorous format to make sure you are not forgetting pieces of information. This is achieved via the "article card" concept, which ensures that your article has the best visibility. The system only accepts clones (ESTs, cDNAs) that have been submitted to Genbank. If this is not your case, contact the curator to find a solution. The developmental stages are as in the standard ascidian developmental table (Hotta et al 2007 Developmental Dynamics), except that Aniseed compresses tailbud stages into 4 stages only (initial, early, mid, late).

You can enter data obtained from experiments via Aniseed Curator. For that, contact the Aniseed Team to get an individual password before entering data. A detailed manual available here was written to help you to enter every type of data.

You can also use a modified Excel spreadsheet for larger submission. Thanks to these files, you can enter expression profiles in wild type or mutant condition, morphological phenotypes and studies of regulatory sequences. Once the excel forms are filled, a parser enter automatically data from the files into the database. You can also use these files to organize and store expression data. You are provided with a template that specifies the required information and facilitates data entry via keyword selection lists and a detailed user guide.

• Excel file to enter expression data in wild type condition
• Excel file to enter expression data in deregulated molecule context
• Excel file to enter expression data in perturbed anatomical context
• Excel file to enter a morphological phenotype
• Excel file to enter cis-regulatory region information
• Quick start to use the Excel Files

AMIS, The Article Minimum Information Standard

The curation process is significantly slowed down by missing information in the articles analyzed. The identity of the clones used to generate ISH probes and the precise sequences tested in reporter assays constituted the most frequent omissions. 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 section describes for each experiment the mandatory (and useful) 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).

Minimal information to describe a wild-type spatio-temporal expression pattern

Mandatory information

• Developmental stage at which the expression was determined, according to the table of Hotta et al. (2007)
• Clone(s) used to synthesize the in situ hybridization probes used in the experiment, transgenic construct in the case of electroporations, or antibody, with reference, used in immunohistochemistry.
• Annotation: use the anatomical ontology of Aniseed to describe the territories of expression in legends and main text.

Additional useful information

• Picture, comments in figure legend.

Minimal information to describe a molecular perturbation

Mandatory information

• Identity of the deregulated molecule: The biological name of the gene can be ambiguous. It is preferable to indicate the corresponding gene/transcript model deregulated with a preference for KH (Satou et al., 2008) models, followed by JGI v1.0 and ENSEMBL models.
• Type of interference with gene function: gain-of-function or loss-of-function.
• Molecular tool used to deregulate the gene, with either reference of a previous study using this tool (eg FGF9/16/20 MO described in Imai et al., 200XX), or the precise sequence (MOs, mRNAs) or origin (Small molecules) of the tool.
• Stage of onset of the perturbation (eg. time of injection for morpholinos).

Minimal information to describe an anatomical perturbation

Mandatory information

• Time of perturbation: Hotta stage when the structure(s) was/were removed or when the explants(s) was/were isolated.
• Removed anatomy part or explant: use the Aniseed anatomical dictionary to describe the removed anatomy part(s) or the type of explant isolated.

Minimal information to describe a molecular phenotype
Molecular or anatomical perturbations can lead to molecular phenotypes, consisting in alteration in gene expression patterns.

Mandatory information

• Description of the molecular or anatomical perturbation leading to the phenotype.
• Developmental stage at which the expression of the target gene was determined, according to the developmental table of Hotta et al. ( 2007)
• Clone(s) used to synthesize the in situ hybridization probes used in the experiment, transgenic construct in the case of electroporations, or antibody, with reference, used in immunohistochemistry.
• Wild-type control: Clearly indicate the expression profile of the wild type control determined in the same ISH or immunocytochemistry experiment as the experimental sample.
• Annotation: use the anatomical ontology of Aniseed to describe the territories in which the expression pattern of the target gene differs between wild-type control and experimental sample.

Additional useful information

• Pictures of embryos with affected and wild-type expression patterns, comments in figure legend.

Minimal information to describe a morphological phenotype
Molecular or anatomical perturbations can lead to morphological phenotypes, that are described without reference to affected gene expression patterns.

Mandatory information

• Description of the molecular or anatomical perturbation leading to the phenotype.
• Developmental stage at which the expression of the phenotype was examined, according to the developmental table of Hotta et al. ( 2007)
• Part of body/embryo affected (e.g. Tail, trunk, sensory vesicle), if possible using the Aniseed anatomical dictionary or of the embryological process affected (eg gastrulation, neurulation, tail extension)
• Qualifier of the type of phenotype observed in the indicated dictionary (eg disorganized, short, defective)

Additional useful information

• Pictures of affected and wild-type embryos, comments in figure legend.

Minimal information to describe a regulatory region

Mandatory information

• Regulated gene(s), when known: indicate the KH gene model reference (eg KH.C4.84) in addition to the "common name" (eg Ci-otx).
• Name of the region: Please respect the following format for region names: ci-"common gene name" "start of region/end of region e.g. ci-Otx -4037/+31. In the absence of well defined TSS, the definition of +1 should be clearly indicated in the text. Using different naming conventions will lead to a renaming of the regions you studied according to the above criteria and may delay publication of cis-regulatory information in Aniseed.
• Name of constructs: Please respect the following format: "p" (for plasmid)"region name" name"" basal promoter name" :: " reporter gene" e.g. "pfog -214/-74 pbra::NLS LacZ"
• Sequence of genomic fragments in electroporated constructs: Because of the high level of polymorphism in ascidian genomes, genomic fragments tested by electroporation may depart from the consensus genome sequence (Dehal et al., 2001). Please indicate the sequence in supplemental information, or submit these directly to Genbank or Aniseed.
• Sequences of artificial or mutated constructs (ie synthetic DNA not corresponding to a part of the genome): clearly indicate the sequence of the region in the Methods section or supplemental information. regions with internal deletions or mutations of binding sites should be named as follows: insert either "delta" followed by the deleted sequence (eg "ZicL -658bp/codon 7 delta -205/-127" ) or "mutated" following the affected binding site eg "Otx -1541bp/-1417bp Ets1-2 mutated"
• Upstream factors binding sites and identity: Clearly indicate the functional binding sites in tested sequences and the upstream factors that bind them (when known) using the relevant KH gene identifier in addition to their common name.

MISFISHIE Exchange Format
To facilitate data transfer between expression databases, a MISFISHIE-compliant XML data format has been developed that can be used to format already existing datasets. Thus, as it was done for the MIAME project, a MISFISHIE Document Type Definition (DTD) was defined for three expression databases:
- ANISEED
- COMPARE
- 4DXpress
This document contains a set of rules that are following the MISFISHIE standard. This DTD available here defines the guideline to follow for being MISFISHIE compliant.
Example:
Export of in situ Hybridization from Aniseed here.