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BioNames update - matching taxon names to classifications

On eof the things BioNames will need to do is match taxon names to classifications. For example, if I want to display a taxonomic hierarchy for the user to browse through the names, then I need a map between the taxon names that I've collected and one or more classifications. The approach I'm taking is to match strings, wherever possible using both the name and taxon authority. In many cases this is straightforward, especially if there is only one taxon with a name. But often we have cases where the same name has been used more than once for different taxa. For example, here is what ION has for the name "Nystactes".
Nystactes Bohlke2735131
Nystactes2787598
Nystactes Gloger 18274888093
Nystactes Kaup 18294888094


If I want to map these names to GBIF then these are corresponding taxa with the name "Nystactes":
Nystactes Böhlke, 19572403398
Nystactes Gloger, 18272475109
Nystactes Kaup, 18293239722


Clearly the names are almost identical, but there are enough little differences (presence or absence of comma, "o" versus "ö") to make things interesting. To make the mapping I construct a bipartite graph where the nodes are taxon names, divided into two sets based on which database they came from. I then connect the nodes of the graph by edges, weighted by how similar the names are. For example, here is the graph for "Nystactes" (displayed using Google images:


I then compute the maximum weighted bipartite matching using a C++ program I wrote. This matching corresponds to the solid lines in the graph above.

In this way we can make a sensible guess as to how names in the two databases relate to one another.

BioNames update - API documentation

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One of the fun things about developing web sites is learning new tricks, tools, and techniques. Typically I hack away on my MacBook, and when something seems vaguely usable I stick it on a web server. For BioNames things need to be a little more formalised, especially as I'm collaborating with another developer (Ryan Schenk). Ryan is focussing on the front end, I'm working on the data (harvesting, cleaning, storing).

In most projects I've worked on the code to talk to the database and the code to display results have been the same, it was ugly but it got things. For this project these two aspects have to be much more cleaning separated so that Ryan and I can work independently. One way to do this is to have a well-defined API that Ryan can develop against. This means I can hide the sometimes messy details of how to communicate with the data, and Ryan doesn't need to worry about how to get access to the data.

Nice idea, but to be workable it requires that the API is documented (if it's just me then the documentation is in my head). Documentation is a pain, and it is easy for it to get out of sync with the code such that what the docs say an API does and what it actually does are two separate things (sound familiar?). What would be great is a tool that enables you to write the API documentation, and make that "live" so that the API output can be tested against. In other words, a tool like apiary.io.

Apiary.io is free, very slick, and comes with GitHUb integration. I've started to document the BioNames API at http://docs.bionames.apiary.io/. These documents are "live" in that you can try out the API and get live results from the BioNames database.

I'm sure this is all old news to real software developers (as opposed to people like me who know just enough to get themselves into trouble), but it's quite liberating to start with the API first before worrying about what the web site will look like.

New look Biodiversity Heritage Library launched


The new look Biodiversity Heritage Library has just launched. It's a complete refresh of the old site, based on the Biodiversity Heritage Library–Australia site. If you want an overview of what's new, BHL have published a guide to the new look site. Congrats to involved in the relaunch.

One of the new features draws on the work I've been doing on BioStor. The new BHL interface adds the notion of "parts" of an item, which you can see under the "Table of Contents" tab. For example, the scanned volume 109 of the Proceedings of the Entomological Society of Washington now displays a list of articles within that volume:

Newbhl
This means you can now jump to individual articles. Before you had to scroll through the scan, or click through page numbers until you found what you were after. The screenshot above shows the article "Three new species of chewing lice (Phthiraptera: Ischnocera: Philopteridae) from australian parrots (Psittaciformes: Psittacidae)". The details of this article have been extracted from BioStor, where this article appears as http://biostor.org/reference/55323. You can go directly to this article in BHL using the link http://www.biodiversitylibrary.org/part/69723. As an aside, I've chosen this article because it helps demonstrate that BHL has modern content as well as pre-1923 literature, and this article names a louse, Neopsittaconirmus vincesmithi after a former student of mine, Vince Smith. You're nobody in this field unless you've had a louse named after you ;)

BioStor has over 90,000 articles, but this is a tiny fraction of the articles contained in BHL content, so there's a long way to go until the entire archive is indexed to article level. There will also be errors in the article metadata derived from BioStor. If we invoke Linus's Law ("given enough eyeballs, all bugs are shallow") then having this content in BHL should help expose those errors more rapidly.

As always, I have a few niggles about the site, but I'll save those for another time. For noe, I'm happy to celebrate an extraordinary, open access archive of over 40 million pages. BHL represents one of the few truly indispensable biodiversity resources online.

BioNames ideas - automatically finding synonyms from the literature

One of the biggest pains (and self-inflicted wounds) in taxonomy is synonymy, the existence of multiple names for the same taxon. A common cause of synonymy is moving species to different genera in order to have their name reflect their classification. The consequence of this is any attempt to search the literature for basic biological data runs into the problem that observations published at different times by different researchers (e.g., taxonomists, ecologists, parasitologists) may use different names for the same taxon.

Existing taxonomic databases often have lists of synonyms, but these are incomplete, and typically don't provide any evidence why two names are synonyms.

Reading literature extracted form the Biodiversity Heritage Library I'm struck by how often I come across papers such as taxonomic revisions, museum catalogues, and checklists, that list two names as synonyms. Wouldn't it be great if we could mine these to automatically build lists of synonyms?

One quick and dirty way to do this is look for sets of names that have the same species name but different generic names, e.g.

  • Atlantoxerus getulus
  • Sciurus getulus
  • Xerus getulus

If such names appear on the same page (i.e., in close proximity) there's a reasonable chance they are synonyms. So, one of the features I'm building in BioNames is an index of names like this. Hence, if we are displaying a page for the name Atlantoxerus getulus that page could also display Sciurus getulus and Xerus getulus as possible synonyms.

There's a lot more that could be done with this sort of approach. For example, this approach only works if the the species name remains unchanged. To improve it we'd need to do things like handle changes to the ending of a species name to agree with the gender of the genus, and cases where the taxa are demoted to subspecies (or promoted to species).

If we were even clever we'd attempt to parse synonymy lists to extract even more synonyms (for an example see Huber and Klump (PDF available here):

Huber, R., & Klump, J. (2009). Charting taxonomic knowledge through ontologies and ranking algorithms. Computers & Geosciences, 35(4), 862–868. doi:10.1016/j.cageo.2008.02.016

Then there's the broader topic of looking at co-occurrence of taxonomic names in general. As I noted a while ago there are examples of pages in BHL that lists taxonomically unrelated taxa that are ecologically closely associated (e.g., hosts and parasites). Hence we could imagine automatically building host-parasite databases by mining the literature. Initially we could simply display lists of names that co-occur frequently. Ideally we'd filter out "accidental" co-occurrences, such as indexes or tables of contents, but there seems to be a lot of potential in automating the extraction of basic information from the taxonomic literature.

Figuring Out an Accounting Career



What You Can Count On: Job Security

For the 2007 fiscal year, Microsoft reported an annual revenue of $51.2 billion. Behind any company's revenue numbers--big or small--are accountants and financial managers who balance the books. In 2002, the Sarbanes-Oxley Act added further scrutiny to corporate procedures. Between government regulations and the thousands of companies that need to manage finances, the immediate benefit of a career in accounting is a reasonable amount of job security. Additionally, the Bureau of Labor Statistics (BLS) predicts strong growth for accountants and auditors through 2016.

What You Can Take to the Bank: Strong Earnings

Another benefit for an accountant is that the median annual salary for accounting, tax preparation, bookkeeping, and payroll services is $57,020. Going further into the financial services industry, you could become a financial manager for a major corporation and earn in the neighborhood of $105,410 a year according to the BLS. You can also work your way up the corporate ladder to financial director, corporate controller, or even chief financial officer (CFO).

What Education You Need: Accounting Degree and Certification

A college degree and certification are almost essential for advancement and a long term career in accounting. A bachelor's degree in accounting or a finance related topic is a solid start, and earning a Certified Public Accountant (CPA) credential furthers your employability prospects. You can even take it a step-further by earning a specialized certification such as a Certified Management Accountant (CMA), Certified Internal Auditor (CIA), Accredited Tax Advisor (ATA), or other credential. The American Institute of Certified Public Accountants reports on a survey finding that candidates with a professional certification can earn 10% more than other accountants. A graduate degree can also help you stand out from the crowd.

Questions and Answers About Starting an Accounting Career



An accountant plays a very important role in the functioning and efficiency of a corporation. They provide a number of vital business services to clients including the management of financial matters, auditing, and handling tax issues. However, the specific duties performed in an accounting career will differ depending on what field the practitioner works in, be it public accounting, management accounting, government accounting, or internal auditing.

Accountants will generally use computers and special accounting programs to assist them in their duties. Accountants can summarize and organize data in particular formats to make them more suitable for storage or analysis. The programs also remove a lot of the tedious manual work of accounting out of the job. For this reason, accountants will generally have a very high level of competence with computers and many employers will require them to be proficient in these programs to help keep their work accurate.

The environment in which an accountant works will generally vary depending on what field of accounting he/she is in as well as what type of company or organization he/she works for. The vast majority of accountants work in an office setting, often with many other coworkers and colleagues; although, some accountants are self-employed and may be able to work part of their job at home as well. Most accountants work a standard 40-hour week; though, there are exceptions especially in the case of tax specialists and self-employed accountants who may work longer hours during certain times of the year.

Public accounting firms often send their accountants to their clients' place of work or residence to perform audits. In this scenario, there can also be a lot of traveling involved. Accountants who travel often will most likely use a laptop to allow for the increased mobility of their accounting programs, data, and other information needed on the job.

Accountants, regardless of their chosen field, require a proficiency in mathematics as well as business. Many accountants are unlicensed, especially in the fields of government accounting, management accounting, and internal auditing. A bachelor's degree in accounting or a related field is required to become licensed as a Certified Public Accountant (CPA), Public Accountant (PA), Registered Public Accountant (RPA), or Accounting Practitioner (AP). Some companies will require their accountants to hold master's degrees as well.

There is a large demand for accountants, and as more businesses are created in the coming years, the demand is expected to increase. The rapid expansion of business is also expected to have a large effect on the types of responsibilities accountants will have. Nevertheless, these jobs can be very competitive, and many businesses are increasing their standards by which they hire and the qualifications they demand.

Accountants who have a great knowledge of computers and many different accounting software will have a better change of employment. Also, those who have more education, training, and experience will also have an edge in the job market. It is also important for accountants to demonstrate interpersonal skills as this will also help them perform their job more effectively and get along better with clients.

How to Start Your Accounting Career



You want to be an accountant. You love numbers, maths and money. So, how do you get started? Where do you go to get certified so that your services will be in demand? If you do not have any recognised qualifications, your clients will not be able to know if your standards meet their requirements. People hire Chartered Certified Accountants with a full practicing certificate because they know that they can trust in their expertise.

Any old accountancy certification will not do. You need an internationally recognised global qualification to compete in today's industry, and the ACCA qualification fits this demand perfectly. The Association of Chartered Certified Accountants (ACCA) is the world's largest international accountancy body, with over 300,000 members and students in more than 160 countries. Founded in 1904, ACCA has over 100 years of history as a leader in the development of the global accountancy profession. The United Nations has chosen the ACCA syllabus as the basis of its global accountancy curriculum and the ACCA qualification is well recognised in an ever-growing list of countries including the USA, Canada, the United Kingdom, the European Union, Australia, New Zealand, South Africa, China, Singapore, Malaysia and Pakistan. Many ACCA graduates work in premier companies such as British Airways and Price Waterhouse Coopers.

The syllabus spans 16 topics each with its own examination to test your competency in that subject. It usually takes 2 years for a student to obtain the ACCA qualification. This is broken up into the "Fundamentals" stage that consists of 9 papers and the "Professional" stage that consists of 3 papers and a choice of 4 options. With so many examinations to pass, self-study can be difficult. The good news is that there are many professional accounting and finance schools such as FTMS Global that offer ACCA courses. The better ones have a cast of highly qualified and experienced lecturers who are ACCA-certified. These teachers know what the ACCA syllabus requires and can dramatically increase your chances of passing the examinations. Definitely, it is highly recommended to enlist the aid of a mentor who can show you the ropes.

After qualifying as a Chartered Certified Accountant by passing the examinations, to obtain the practising certificate you must have had sufficient experience in a practising accountant's office. On top of all that, you must continue to keep yourself updated by attending courses on a regular basis. The ACCA is the only accountancy body that provides a disciplinary system which offers remedy if any ACCA member breaches its high standards.

Once you obtain the ACCA certification, your clients know with certainty that they can depend on:

- Your integrity

- Your absolute respect for the confidentiality of your client's affairs

- Your knowledge and expertise

- The fact that there is a regulatory body who will ensure that standards are maintained

- The fact that you must operate within a strict framework of rules and ethics

The entry requirements of the ACCA qualification are 2 A-Level passes or a bachelor's degree from a recognised university. If you do not meet this requirement, you may opt to go for the open-entry route by taking the Certified Accounting Technician (CAT) qualification first. Upon completion of the CAT course, you may progress to take the ACCA qualification.