Message-ID: <> Subject: Exported From Confluence MIME-Version: 1.0 Content-Type: multipart/related; boundary="----=_Part_414_1658505719.1566121861663" ------=_Part_414_1658505719.1566121861663 Content-Type: text/html; charset=UTF-8 Content-Transfer-Encoding: quoted-printable Content-Location: file:///C:/exported.html ZFIN Data Submissions

ZFIN Data Submissions

ZFIN welcomes direct data submissions. If you would like to make= your unpublished expression or phenotype data available to the community, = you can submit this data to ZFIN using the Phenote program.  A detaile= d description of the data types that can be submitted to ZFIN, along with d= ata submission templates have been reported in Howe et al., 2016. &= nbsp;These resources can help guide data collection for submission to ZFIN.=

Phenote allows you to save and load your expression or phenotype annotat= ions in a tab-delimited file that can be read by Microsoft Excel. Phenote i= s advantageous because it uses ZFIN anatomy and phenotype ontology terms, s= o you (and ZFIN) don't have to go looking for them. It also allows basic br= owsing for terms, which should expedite annotation. We hope that you will f= ind this new tool helpful for annotation of mutant phenotypes or gene expre= ssion.

You can download the current stable Phenote release or check out the more recent beta versions. The current Phenote beta is known to work on Windo= ws XP, MacOSX, MacOSXI.

Instructions for using Phenote to submit phenotype or expression dat= a to ZFIN:

Phenote takes a couple of minutes to start up, because it downloads the = most current Gene and zebrafish anatomy ontologies. Phenote requires Java on = your machine. Phenote opens dialog windows in the background as it loads an= d needs you to interact with these windows to finish loading. Mac users who= , for security reasons, use a non-administrator user account should install= Phenote somewhere in their home folder (i.e., not in the Applications fold= er). The beta versions are fully functional, but there are always some roug= h edges in betas - sometimes rows in the main Annotation Table seem to be g= rayed-out. Clicking on the missing rows will reveal them again. You may als= o need to configure your firewall software to allow Phenote to access the n= ewest versions of the ontologies.

After starting up Phenote, under Settings at the top, choose zfin-phenot= ype or zfin-expression from the "Set Configuration..." menu. Then restart P= henote.

Phenote is an ontology smart spreadsheet that can save in a tab-delimite= d format which is compatible with MS Excel. Each line at the bottom is one = annotation. As you type in the fields in the upper half, you will see your = annotation filled in the bottom half. To create a new annotation, click on = the new button at the bottom. You can delete or undo with the buttons at th= e bottom, and simply clicking on a line will bring up the annotation at the= top of Phenote.

For pub, Image file, gene, and genotype (line name) you can type in free= text. ZFIN can help you update these later. If you are submitting images t= he file names need to be unique. ZFIN recommends using a combination of fea= ture name and stage to give each file a unique name e.g. b215prim5a, b215pr= im5b b215day5a.

The entity is the anatomical structure in which you see the phenotype or= expression. You can choose between two ontologies, the ZFIN anatomy ontolo= gy, or the Gene Ontology Cellular Component ontology. There is a type ahead= feature for this field, and you can view details about a given term in the= term info box to the right. To make a more complex structure called a post= -composed entity, you hit the comp button, and get three fields. You might = want something like, GOcc:mitochondrion part_of ZF:neuron. This means that = the expression is in the mitochondria in neurons. The stages are standard f= rom our stage ontology. You may wish use the EBI lookup tool and/or the ZFIN Anatomy / GO search to find terms by context if you = cannot locate them through the Phenote interface. If you cannot find the ze= brafish structure you need please fill out the term request form. Please in= clude the structure name, the stage the structure becomes apparent and any = other useful information so we can update the ontology.

For phenotypic qualities, you will choose a term from the PATO = ontology. The quality is the adjective that describes the phenotype. Th= is ontology can also be browsed at the ontology lookup service if you ca= nnot find the term you are looking for. Please contact either ZFIN or submit to the <= a class=3D"external-link" href=3D" =3D76834&atid=3D595654">PATO tracker if the term you need isn't in = PATO.

You can make multiple annotations for the same line; for instance, if yo= u want to record phenotype in more than one structure. Just hit the Duplica= te button (two overlapping +) and change the field that is different.

To save, hit the "Save Data" button at the bottom, and your data will be= saved as a tab-delimited file.

Visit the Phenote FAQ for answers to frequently asked questions or email <= a class=3D"external-link" href=3D"">ZFIN with q= uestions, test files or your final data submission files.