Official Experimental Hierarchy

September 12, 2013 | Posted by Fraser Tan in Company, Lab Admin Tools, Science Exchange News |

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Over the past two years, Science Exchange has compiled and listed over 1800 unique services available for request. With services ranging in fields from biological methods to chemical analysis to microfabrication, we felt it was time to categorize these services by some logical order – a true experimental services hierarchy.

After several months of research and diligence, we have just launched the Official Experimental Hierarchy on Science Exchange. This new Hierarchy will interface with and improve the search functionality on Science Exchange, allowing users to quickly find the services they are looking for. Based on their search terms, users will enter the tree at the lower levels, and be able to browse around the nearby branches to identify the exact technique they are looking for, or find related techniques that best suits their needs. It will also provide a platform to ensure that our requesters and providers are speaking on the same terms.

Exploring The Experimental Hierarchy

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The first major branch-point of the Experimental Hierarchy is between Analytical Services and Experimental Services.

The Analytical Services branch is meant to encompass all services that are “in silico”, such a bioinformatics, data analysis and management, consulting, writing help, figure preparation, software development, etc. Its subclass Analysis and Design comprises most of the analytical services offered, including Computational Modeling, Image Analysis, and analysis of nucleic acid data such as next generation sequencing data analysis.

The Experimental Services branch in turn encompasses wet-lab techniques, like next generation sequencing, peptide synthesis, high performance liquid chromatography and high magnetic field processing, among others. Each branch is further subdivided based both on area of application.

Subclasses of Experimental Services are quite extensive. The subclass Biological Methods contains services most useful to the life sciences, including animal cloning and transgenic development services, cell based assays, and analysis of nucleic acids and proteins. The subclass Imaging contains all imaging related services, both pictographic (Recorded Image) and illustrative (Schematics). Microscopy, magnetic resonance imaging, ultrasound and x-ray are examples of pictographic imaging services, while Schematics include computer graphics, fine art graphics and illustrations. Histological Methodology covers most of the tissue staining services, including tissue preparation services such as embedding and sectioning, as well as histological stains, antibody stains and in situ hybridization (found under Visualizing Gene and Protein Expression).

To explore the Experimental Hierarchy yourself, start with the Experimental Services at:–2 

Generating The Experimental Hierarchy

Building the Experimental Hierarchy involved the efforts of multiple parties and resources.

Initially, we explored existing ontology frameworks to see if a tree for experimental services already existed; none did. In order to generate the overall structure of the hierarchy, we enlisted the help of Oxbridge Biotech Roundtable (OBR). The OBR team consisted of experts across multiple scientific disciplines: Charlotte Chen (Stanford), Jeroen Blokhius (Stanford), Elly Chow (CalTech), Farhan Baluch (USC), Markus Hauschild (CalTech), Sapna Jain (USC), Sum-yang Ng (USC), team lead Sicong Li (USC), with expert advice from Kim Durante, a metadata expert from Stanford University libraries.

After receiving Science Exchange’s list of originally 1,800 unstructured services, the team examined existing ontologies (the Quantitative Imaging Biomarker ontology, Eagle-I Research Resource ontology, the Measurement Method ontology and the Ontology for Biomedical Investigations, among others) and used their own domain expertise to build the major branches of the Experimental Hierarchy based on underlying technology and overall purpose.

Moving Forward

This Experimental Hierarchy  is only the beginning. In the coming weeks, we will be refining and pruning the tree further, consolidating synonymous service offerings and standardizing service names to ensure our requesters and providers are speaking on the same terms.

In the future, we hope to add new features to improve the function of the hierarchy, such as multiparent classes to classify techniques that are hybrids of two distinct technologies or have applications in multiple different areas. This hierarchy is an ongoing effort, evolving and growing to fit the needs of our researchers and providers, and we welcome any and all feedback.

Feel free to contact me at [email protected] if you have any feedback or recommendations.

About the author

Fraser supports our customers on Science Exchange. She completed her graduate and postdoctoral studies at Stanford University and served on the Marketing and Development Team for before joining Science Exchange.

About Science Exchange

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