From the Book:
“Clean code that works” is Ron Jeffries’ pithy phrase. The goal is clean code that works, and for a whole bunch of reasons:
Clean code that works is a predictable way to develop. You know when you are finished, without having to worry about a long bug trail.Clean code that works gives you a chance to learn all the lessons that the code has to teach you. If you only ever slap together the first thing you think of, you never have time to think of a second, better, thing. Clean code that works improves the lives of users of our software.Clean code that works lets your teammates count on you, and you on them.Writing clean code that works feels good.But how do you get to clean code that works? Many forces drive you away from clean code, and even code that works. Without taking too much counsel of our fears, here’s what we do—drive development with automated tests, a style of development called “Test-Driven Development” (TDD for short). 
In Test-Driven Development, you:
Write new code only if you first have a failing automated test.Eliminate duplication.

Two simple rules, but they generate complex individual and group behavior. Some of the technical implications are:You must design organically, with running code providing feedback between decisionsYou must write your own tests, since you can’t wait twenty times a day for someone else to write a testYour development environment must provide rapid response to small changesYour designs must consist of many highly cohesive, loosely coupled components, just to make testing easy

The two rules imply an order to the tasks ofprogramming:
1. Red—write a little test that doesn’t work, perhaps doesn’t even compile at first
2. Green—make the test work quickly, committing whatever sins necessary in the process
3. Refactor—eliminate all the duplication created in just getting the test to work


Red/green/refactor. The TDD’s mantra.

Assuming for the moment that such a style is possible, it might be possible to dramatically reduce the defect density of code and make the subject of work crystal clear to all involved. If so, writing only code demanded by failing tests also has social implications:
If the defect density can be reduced enough, QA can shift from reactive to pro-active workIf the number of nasty surprises can be reduced enough, project managers can estimate accurately enough to involve real customers in daily developmentIf the topics of technical conversations can be made clear enough, programmers can work in minute-by-minute collaboration instead of daily or weekly collaborationAgain, if the defect density can be reduced enough, we can have shippable software with new functionality every day, leading to new business relationships with customers


So, the concept is simple, but what’s my motivation? Why would a programmer take on the additional work of writing automated tests? Why would a programmer work in tiny little steps when their mind is capable of great soaring swoops of design? Courage.
Courage
Test-driven development is a way of managing fear during programming. I don’t mean fear in a bad way, pow widdle prwogwammew needs a pacifiew, but fear in the legitimate, this-is-a-hard-problem-and-I-can’t-see-the-end-from-the-beginning sense. If pain is nature’s way of saying “Stop!”, fear is nature’s way of saying “Be careful.” Being careful is good, but fear has a host of other effects:
Makes you tentativeMakes you want to communicate lessMakes you shy from feedbackMakes you grumpy

None of these effects are helpful when programming, especially when programming something hard. So, how can you face a difficult situation and:
Instead of being tentative, begin learning concretely as quickly as possible.Instead of clamming up, communicate more clearly.Instead of avoiding feedback, search out helpful, concrete feedback.(You’ll have to work on grumpiness on your own.) 

Imagine programming as turning a crank to pull a bucket of water from a well. When the bucket is small, a free-spinning crank is fine. When the bucket is big and full of water, you’re going to get tired before the bucket is all the way up. You need a ratchet mechanism to enable you to rest between bouts of cranking. The heavier the bucket, the closer the teeth need to be on the ratchet.

The tests in test-driven development are the teeth of the ratchet. Once you get one test working, you know it is working, now and forever. You are one step closer to having everything working than you were when the test was broken. Now get the next one working, and the next, and the next. By analogy, the tougher the programming problem, the less ground should be covered by each test.

Readers of Extreme Programming Explained will notice a difference in tone between XP and TDD. TDD isn’t an absolute like Extreme Programming. XP says, “Here are things you must be able to do to be prepared to evolve further.” TDD is a little fuzzier. TDD is an awareness of the gap between decision and feedback during programming, and techniques to control that gap. “What if I do a paper design for a week, then test-drive the code? Is that TDD?” Sure, it’s TDD. You were aware of the gap between decision and feedback and you controlled the gap deliberately.

That said, most people who learn TDD find their programming practice changed for good. “Test Infected” is the phrase Erich Gamma coined to describe this shift. You might find yourself writing more tests earlier, and working in smaller steps than you ever dreamed would be sensible. On the other hand, some programmers learn TDD and go back to their earlier practices, reserving TDD for special occasions when ordinary programming isn’t making progress.

There are certainly programming tasks that can’t be driven solely by tests (or at least, not yet). Security software and concurrency, for example, are two topics where TDD is not sufficient to mechanically demonstrate that the goals of the software have been met. Security relies on essentially defect-free code, true, but also on human judgement about the methods used to secure the software. Subtle concurrency problems can’t be reliably duplicated by running the code.

Once you are finished reading this book, you should be ready to:
Start simplyWrite automated testsRefactor to add design decisions one at a time

This book is organized into three sections.
An example of writing typical model code using TDD. The example is one I got from Ward Cunningham years ago, and have used many times since, multi-currency arithmetic. In it you will learn to write tests before code and grow a design organically.An example of testing more complicated logic, including reflection and exceptions, by developing a framework for automated testing. This example also serves to introduce you to the xUnit architecture that is at the heart of many programmer-oriented testing tools. In the second example you will learn to work in even smaller steps than in the first example, including the kind of self-referential hooha beloved of computer scientists.Patterns for TDD. Included are patterns for the deciding what tests to write, how to write tests using xUnit, and a greatest hits selection of the design patterns and refactorings used in the examples.

I wrote the examples imagining a pair programming session. If you like looking at the map before wandering around, you may want to go straight to the patterns in Section 3 and use the examples as illustrations. If you prefer just wandering around and then looking at the map to see where you’ve been, try reading the examples through and refering to the patterns when you want more detail about a technique, then using the patterns as a reference.

Several reviewers have commented they got the most out of the examples when they started up a programming environment and entered the code and ran the tests as they read.

A note about the examples. Both examples, multi-currency calculation and a testing framework, appear simple. There are (and I have seen) complicated, ugly, messy ways of solving the same problems. I could have chosen one of those complicated, ugly, messy solutions to give the book an air of “reality.” However, my goal, and I hope your goal, is to write clean code that works. Before teeing off on the examples as being too simple, spend 15 seconds imagining a programming world in which all code was this clear and direct, where there were no complicated solutions, only apparently complicated problems begging for careful thought. TDD is a practice that can help you lead yourself to exactly that careful thought.

Test Driven Development: By Example

Interpreting qualitative data

The IUPHAR/BPS Guide to PHARMACOLOGY (GtoPdb, www.guidetopharmacology.org) and its precursor IUPHAR-DB, have captured expert-curated interactions between targets and ligands from selected papers in pharmacology and drug discovery since 2003. This resource continues to be developed in conjunction with the International Union of Basic and Clinical Pharmacology (IUPHAR) and the British Pharmacological Society (BPS). As previously described, our unique model of content selection and quality control is based on 96 target-class subcommittees comprising 512 scientists collaborating with in-house curators. This update describes content expansion, new features and interoperability improvements introduced in the 10 releases since August 2015. Our relationship matrix now describes ∼9000 ligands, ∼15 000 binding constants, ∼6000 papers and ∼1700 human proteins. As an important addition, we also introduce our newly funded project for the Guide to IMMUNOPHARMACOLOGY (GtoImmuPdb, www.guidetoimmunopharmacology.org). This has been 'forked' from the well-established GtoPdb data model and expanded into new types of data related to the immune system and inflammatory processes. This includes new ligands, targets, pathways, cell types and diseases for which we are recruiting new IUPHAR expert committees. Designed as an immunopharmacological gateway, it also has an emphasis on potential therapeutic interventions.

/pdf/the-iuphar-bps-guide-to-pharmacology-in-2018-updates-and-166fvz11dp.pdf

The IUPHAR/BPS Guide to PHARMACOLOGY in 2018: updates and expansion to encompass the new guide to IMMUNOPHARMACOLOGY

2005년 대한 생화학·분자생물학회 하계학술대회를 다녀와서

In this paper we provide a comprehensive introduction to knowledge graphs,
which have recently garnered significant attention from both industry and
academia in scenarios that require exploiting diverse, dynamic, large-scale
collections of data. After some opening remarks, we motivate and contrast
various graph-based data models and query languages that are used for knowledge
graphs. We discuss the roles of schema, identity, and context in knowledge
graphs. We explain how knowledge can be represented and extracted using a
combination of deductive and inductive techniques. We summarise methods for the
creation, enrichment, quality assessment, refinement, and publication of
knowledge graphs. We provide an overview of prominent open knowledge graphs and
enterprise knowledge graphs, their applications, and how they use the
aforementioned techniques. We conclude with high-level future research
directions for knowledge graphs.

Knowledge Graphs

FaBiO and CiTO

In this paper we address the issue of identifying the concepts in an ontology, which best summarize what the ontology is about. Our approach combines a number of criteria, drawn from cognitive science, network topology, and lexical statistics. In the paper we show two versions of our algorithm, which have been evaluated against the results produced by human experts. We report that the latest version of the algorithm performs very well, exhibiting an excellent degree of correlation with the choices of the experts. While the generation of automatic methods for ontology summarization is an interesting research issue in itself, the work described here also provides a basis for novel approaches to a variety of ontology engineering tasks, including ontology matching, automatic classification, ontology modularization, and ontology evaluation.

/pdf/identifying-key-concepts-in-an-ontology-through-the-4f0kmm1bu0.pdf

Identifying Key Concepts in an Ontology, through the Integration of Cognitive Principles with Statistical and Topological Measures

In this paper we introduce Graffoo, i.e., a graphical notation to develop OWL ontologies by means of yEd, a free editor for diagrams.

/pdf/modelling-owl-ontologies-with-graffoo-5917dzadsx.pdf

Modelling OWL Ontologies with Graffoo

Over the past eight years, we have been involved in the development of a set of complementary and orthogonal ontologies that can be used for the description of the main areas of the scholarly publishing domain, known as the SPAR (Semantic Publishing and Referencing) Ontologies. In this paper, we introduce this suite of ontologies, discuss the basic principles we have followed for their development, and describe their uptake and usage within the academic, institutional and publishing communities.

The SPAR Ontologies

The availability in machine-readable form of descriptions of the structure of documents, as well as of the document
discourse (e.g. the scientific discourse within scholarly articles), is crucial for facilitating semantic publishing and the overall
comprehension of documents by both users and machines. In this paper we introduce DoCO, the Document Components Ontology,
an OWL 2 DL ontology that provides a general-purpose structured vocabulary of document elements to describe both structural and
rhetorical document components in RDF. In addition to describing the formal description of the ontology, this paper showcases its
utility in practice in a variety of our own applications and other activities of the Semantic Publishing community that rely on DoCO
to annotate and retrieve document components of scholarly articles.

/pdf/the-document-components-ontology-doco-3pgqzg7r6m.pdf

Silvio Peroni

Papers

FaBiO and CiTO

Identifying Key Concepts in an Ontology, through the Integration of Cognitive Principles with Statistical and Topological Measures

Modelling OWL Ontologies with Graffoo

The SPAR Ontologies

The Document Components Ontology (DoCO)