Open-source toolkit for creating and reusing high-quality spreadsheets.

Markup syntax for spreadsheets

ObjTables provides simple markup for indicating the class and attribute encoded into each worksheet and column of each worksheet (XLSX file or collection of CSV or TSV files).

Schemas for spreadsheets

ObjTables provides a simple format for describing the types of objects encoded in a spreadsheet, their attributes, and their possible relationships.

High-level software tools

ObjTables provides software for using schemas to parse, validate, compare, compose, and analyze annotated spreadsheets.

Publishing re-usable supplementary spreadsheets

Although supplementary spreadsheets contain valuable data, supplementary spreadsheets are hard to reuse because they often contain errors and often capture data ad hoc.

ObjTables enables authors to create high-quality datasets that are both human- and machine-readable: (a) authors can use ObjTables to debug their data, (b) authors can use ObjTables to pretty print data with tables of contents and inline help, (c) authors can publish schemas for parsing their data, and (d) readers can use these schemas to parse and analyze published data with minimal effort.

Sharing re-usable data and models

Research often involves novel datasets and models that require new formats. Unfortunately, the substantial effort needed to reuse these custom formats is a frequent barrier to collaboration.

ObjTables makes it easier to share data and models with collaborators by (a) enabling researchers to clearly describe the structure of their data or model with a schema, (b) enabling researchers to capture metadata about their data or model, (c) providing researchers software tools for validating their data, and (d) enabling collaborators to use these schemas to quickly parse data from colleagues.

Building and analyzing complex datasets and models

Many fields aim to understand how behaviors emerge from complex networks. This often requires integrating diverse data. For example, systems biology aims to understand how cellular behavior emerges from genotype, often using genomics and other data. Spreadsheets are a popular tool for merging data because they are easy to use. However, spreadsheets only support a few data types, and spreadsheets have limited support for multi-dimensional data. In addition, it is difficult to debug spreadsheets.

ObjTables makes it easy to build, validate, and analyze complex datasets: (a) users can use spreadsheets to assemble diverse data, (b) users can quickly define schemas for their data, and (c) users can use these schemas to validate their data and parse it into object-oriented data structures for further analysis in languages such as Python. For example, we have used ObjTables to integrate data about the biochemistry of H1 human embryonic stem cells.

ObjTables also makes it easy to build datasets iteratively over time by helping users revision data with Git and migrate their data as they revise their schemas.

Defining formats for new types of data and predictive computational models

New areas of science often require new types of data and new kinds of predictive computational models. In turn, this often requires new formats to capture these data and models, and new software for working with these formats. Creating these formats is often an obstacle for new domains that have limited resources. Furthermore, evolving these formats as new approaches emerge is challenging because this often requires updating the software tools and converting old files to the new format.

ObjTables addresses this issue by making it easy to define schemas for domain-specific data and providing software tools for parsing, manipulating, and validating data encoded in these schemas. For example, we have used ObjTables to create, WC-KB , a format for the experimental omics, biochemical, and physiological data needed to model cellular biochemistry. We have also used ObjTables to create, WC-Lang , a format for whole-cell models of all of the biochemical activity in a cell. Creating these formats required minimal code.