Chitty taxonomy boot camp best practices final 2017 oct
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The document discusses the development of an in-house taxonomy database over several decades. It began in 1991 with keywords created by the CEO and has expanded to nearly 1,600 concepts today. The taxonomy is used to organize an internal database and public website on genomic glossaries. Maintaining and updating the taxonomy to integrate new topics and ensure interoperability remains an ongoing challenge. Lessons learned include the importance of modularity, descriptive definitions, and choosing software based on scalability and return on investment.
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Chitty taxonomy boot camp best practices final 2017 oct
- 1. Taxonomy for Emerging Technologies: Mary Chitty, MSLS, Library Director & Taxonomist, Knowledge & Information Services Cambridge Healthtech, Needham MA | www.healthtech.com mchitty@healthtech.com 781 972-5416 | www.genomicglossaries.com TODAY’S SCIENCE FICTION CAN BE TOMORROW’S SCIENCE A Division of Cambridge Innovation Institute
- 2. In-house database taxonomy Home-grown SQL database 1991 CEO created structure for keywords – Still involved with identifying and creating new terms 2011 Major reorganization into 25 top level categories 2017 Nearly 1,600 concepts and synonyms Database 2.0 in planning Looking into new software options Public website www.genomicglossaries.com SharePoint intranet 2015 Company migrated to SharePoint intranet 2017 Summer Knowledge & Information Services portal launched Developing resources on using and training about in-house keywords and database All very technical complex terminology 1999 Started as a small glossary based on content from in-house taxonomy 2000 Launched as website 2001 Renamed Glossaries & Taxonomies June Reviewed by Science magazine – a nice surprise! MyTaxonomies
- 3. CaseStudy Search works best IF: 1. You know what to call what you're looking for AND 2. You know what you're looking for exists. Often neither one is certain for my topics. So … 1999, created glossaries on DNA and proteins for new market research products. Really interested in poly-hierarchical and non-hierarchical relationships -- not easily curated! 2000, when websites were still new, realized this could be a solution to update and share my terms. This website could be valuable to others. My company is in the information overload business, but we get overloaded too. In 2017, major Updates including Ontologies & Taxonomies. http://www.genomicglossaries.com/content/ontologies.asp www.GenomicsGlossaries.com
- 4. Start small Because you’re going to make changes Call projects prototype/s or proof/s of concept as long as possible Break daunting project revisions and updates into small manageable chunks Look for quick wins Maximum effect with limited effort More complicated projects can come later Knowledge and credibility gained by rapid prototyping Seek metrics feedback anywhere and everywhere Qualitative and quantitative Google Analytics for usage metrics Welcome questions and emails from users Look for reviews and accolades BestPractices to Start
- 5. Both NIH through the Big Data to Knowledge Program and the European Commission with Horizon 2020 have allocated considerable resources to making data FAIRer. FAIR DATA FAIR Data Principles, 2017 short with link to long version https://www.force11.org/group/fairgroup/fairprinciples FAIR Guiding Principles for scientific data management and stewardship Sci Data. 2016; 3: 160018. Published online 2016 Mar15. doi: 10.1038/sdata.2016.18 https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4792175/ Opportunities fortaxonomists &ontologists Findable Accessible Interoperable Reusable
- 6. LessonsLearned USEFUL INSIGHTS Take advantage of modularity & reusability. Don’t re-invent the wheel. Descriptive not prescriptive definitions, if any. Packaging and labels matter. Taxonomies or ontologies sound sexier than thesauri or controlled vocabularies Taxonomies inherently get more and more granular. Keep editing! REMEMBER Don't try to boil the ocean. 80/20 rule or the Pareto principal Focus on 20% of effort with 80% of usage – not the other way around. Relevance is inherently subjective. What do your users value most?
- 7. MyOngoing Challenges in2017 even after years of experience! MAINTENANCE AND UPKEEP Integration Topics morph in new directions & into new disciplines Interoperability & reusability Huge challenges still Scalability Balance short term & long term needs & goals RETURN ON INVESTMENT Complexity and information overload trade-offs Out-of-the-Box vs. Configurability vs. Customization More programming = more $ - Choose software wisely People can’t buy your products if they don’t know they exist, or where to find them.
- 8. TakeHome Messages Choose challenging – but not impossible projects. Look for allies and buy-in to help make sustainable progress. Use metrics and feedback to measure progress, so you know when you've made some. Share best practices, lessons learned and ongoing challenges. Acknowledge issues nobody has resolved yet, so you don't get discouraged. Focus
Editor's Notes
- Hello and welcome. I'm Mary Chitty and have been the Knowledge Information Services Director at Cambridge Healthtech since it was founded in 1992. My company produces meetings on new and emerging technologies and informatics for pharmaceuticals and biotechnology Ones with commercial potential – often early or seed stage, but beyond basic research.
- My Public website is the taxonomy I’m talking about today. It and the in-house versions are based on the same content Use similar, and highly technical terms and concepts. Am not talking much about my specific subject matter, since that wouldn’t be relevant for some, perhaps many of you. But the challenges of addressing a variety of users, with varying depth of knowledge about a topic may well be of interest. I
- I want to tell you my own taxonomy story When I started working on my glossaries I used Word documents to collect terms and definitions and wanted to share these. Websites were pretty new and I wanted and got one. I thought things would be changing so fast a website would be the only way to keep up. Very little became “wrong” or obsolete, things just got more and more granular. To this day I still refer to some of my original content. But pruning and editing content is a major challenge. I have over 5000 terms , relationships and cross references to manage. My taxonomies inform my own search strategies and helps me offer advice on product titles and SEO. Found I could have longer better conversations with PhD scientists and not run out of things to say after 30 second.. Can ask better questions. Taxonomies are important wayfinding guides for elusive information, and one way to keep up with “synonyms” and variant terms . My taxonomy helps inform my own search strategies and helps me offer advice on product titles and SEO. Trying to understand and coordinate all this technical material... What starts out in one direction and then launch into unexpected directions Found with my taxonomy work I could talk to PhD scientists – both in-house experts and customers, without running out of ideas after 30 seconds. Can ask better questions and understand nuanced relationships. Examples of non-intuitively related terms – personalized medicine, molecular diagnostics, cancer moonshot etc. Still trying to figure out how to categorize microbiomes and how they fit into oncology as well as gut health and antibiotic drug resistance.
- I’m very interested in how individual concepts change in unexpected ways. The science I’m working with is not textbook science, but rather cutting edge to bleeding edge science. But would be happy to have individual discussions about the challenges of highly technical and inter-disciplinary subject taxonomies and ontologies.
- I learned about FAIR data this spring, when Ontoforce, a Belgian semantic search engine company I’ve been collaborating with helped my company organize a FAIR Data hackathon in Boston I love the idea of making data – and content – more Findable, Accessible, Interoperable and Reusable. The European Commission estimates €2 billion in Horizon 2020 funding will be allocated The NIH Data Commons Pilot Phase has an estimated total budget of approximately $55.5 Million Recent estimates of open repositories include “41% of their data are findable and 76% are accessible, but only 38% are interoperable and 18% reusable”. https://www.force11.org/fairprinciples Ontologies – and taxonomies are ways of bridging the data and content in existing {sometimes competing] databases to enable creative reuse of existing data. The reproducibility crisis in science and medicine has made interoperability and reusability challenges more pressing than ever. Taxonomist or ontologist may not be in specific job titles, but our skills are needed. One of the ironies of big data is that we need even more of it. We also need increased attention to data quality and integrity. Some data is so poor it should be discarded. And free-text text-mining offers some of the greatest challenges of all.
- I’m grateful for organizations that try to create prescriptive definitions, but they usually take years to produce results. What I’m working on needs to be categorized RIGHT NOW. Those categories may change. I’m still trying to fully understand microbiomes, which started out in the context of microbes inhabiting our gut and skin and their health effects, but have recently started showing up in cancer research. Labels matter. When I renamed my glossaries "glossaries and taxonomies" our IT guy said “You have real content – not just that marketing fluff!” I love the 80/20 rule. Don’t let the perfect be the enemy of the good. And don’t spend too much time on the 20% no matter how interesting it may be,
- Maintenance and scalability are huge and often underestimated issues. Many decisions involve complex trade-offs. Gardeners know the lure of wanting fast growing plants that look great quickly as you begin your work. But in the long run some plants or trees become invasive and too big – and expensive or impossible to remove. Reusing existing taxonomies or ontologies Often none of them will precisely fit your individual needs. You can use parts of them and learn from them. Not just about technologies. But how people use and implement technologies
- Don’t try to do this all by yourself. Less is more, even though it can take longer to shorten content -- and in some cases threatens to break the moving parts of an existing system. Thank you for your time and attention. My name is Mary Chitty. I will be here the rest of today and all day Tuesday and look forward to talking with you. I’m here to learn and figure out what to do next. Please take one of my cards with my information and links to more about FAIR data.