1. A method for extending and managing a database for an assay by identifying and storing annotation information gathered during planning of an experiment with said database, said method comprising the steps of: (a) creating a directory structure for said database, said directory structure having a plurality of nodes with names; (b) annotating experiment-data to form standardized experiment-data annotation information, wherein the annotating step further comprises the steps of: (i) collecting, by a computer, said standardized experiment-data annotation information, and (ii) transmitting, by the computer, said standardized experiment-data annotation information into said database as part of development of an experiment plan before data collection, wherein said standardized experiment-data annotation information is made available for combination with assay data during data collection; and (c) exporting, by the computer, the standardized experiment-data annotation information to a cooperating instrument for viewing during data collection and for combining with the assay data for subsequent use, wherein the step of annotating experiment-data occurs during development of an experiment plan.