Category Archives: jiscwriteslike.us

Value Add

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Probably the most important thing I discovered in this project was the importance of ‘crowdsourced’ data in filling in the gaps between metadata and common knowledge.

The availability of Wikipedia as a source of random information, although much of it contains inadequate structure to search through with something like dbpedia, is a very important factor for us in improving the metadata and the data that we are putting together to support usage of that metadata. It’s not perfect of course – or perhaps it’s better to say that the imperfect and rough ways in which we use the data are not able to achieve the sorts of results that one might like – but it seems obvious that it’s an invaluable resource for the future.

Other data sources have been invaluable for us as well, particularly DBLP, despite the strong focus on computer science (which, however, means that for training across domains we should probably be looking elsewhere too 🙂 )

Finally, social tags have been less effective for our purposes than one might imagine for one reason, which is that there aren’t an awful lot of them around, and those that are need to be detected by a relatively complex process of resolving title/author into the most popular mirror URI(s).

We’ll be publishing some of the extracted data shortly – boring but useful stuff like lists of institutions, urls, coordinates, enhanced metadata, etc – so hopefully it will come in useful to others!

writeslike.us: Wins and Fails

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Wins:
➢ Getting information such as institution names/URLs from Wikipedia, and widespread use of available web services in general
➢ Extracting names from OAI-DC was easier than expected – although there are still issues with identifying name pair order.
➢ Evidence based learning methods can be applied successfully to the data retrieved to enhance it – getting into FixRep territory. The project has been very useful for the purpose of establishing further use cases for ‘cleaning up’ metadata.
➢ Some interesting work in name / identity disambiguation through statistical clustering analysis. We’re looking at linking extracted info together with formal information such as that made available by the NAMES project.
➢ Storyboards defining the workflow of the system form an effective part of the agile development process, and were very useful for us.
➢ Using an SQL db as the repository was effective once problems with slow queries was addressed through: normalizing data, reviewing db schema design, adding indexes as necessary.

Fails:
➢ Natural Language Tool Kit – didn’t use it for its original purpose. Instead, went back to the Tree Tagger, although this was not specifically trained for the sort of technical document we were analysing.
➢ Text analysis expertise required for this project wasn’t already extant in the team. It would’ve been a good idea to have ensured training for team to make sure we were all on the same page!
➢ Ensure all related documents, URIs, etc, are contained/linked in the project wiki.
➢ Cultural mismatch between research approach to defining requirements/expectations and development requirements/expectations. e.g. who writes the formal requirements document?
➢ Earlier storyboard scenario development would have been helpful, so a good lesson for next time.
➢ Swine flu and its effects were quite severe on this project – our Portugese collaborators were unavailable for quite some time due to a) the danger of traveling to the UK and contracting the virus, and (subsequently to contracting the illness in Portugal) b) the effects of the illness!

Technical standards

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In our project (Writeslike.us) we are using a number of different techniques and tools to make things done.

Coding

As main development languages scripting languages Perl and Python were selected. Python is good for text parsing because language features and external library – Natural language toolkit (NLTK.org) which allow to stem and tag text. The text parsing is non-trivial tasks so for that purpose NLTK use heuristic approach and also offer a training data set for parser to be trained. Perl is native choice for development under Linux and it has powerful set of libraries in CPAN system. In particular XML parsing and full text document crawling functions were written in Perl.
As development tools we are using Eclipse IDE with Perl and Pydev for Perl and Python respectively. In some cases VIM featured text editor is in use. Using such heterogeneous tools implies that project file structure should be flat and simple.

Infrastructure

For running and hosting we are using such proven tools as MySQL and Apache. Subversion (SVN) is used to store and keep track of software versions.

Architecture

The calculation we need to perform to build authors relations network is too resource-intensive to be performed on demand, therefore we need to generated and store database tables with pre-calculated data as some sort of caching approach. Since our project is re-using existing metadata (in Dublin Core (oai-dc, often from qualified DC)) from a repository we were required to add to original project feature list also XML parser and document full text crawler functions.
In order increase usability of the project offered functionality we created a REST interface which enable machine2machine interface. The interface enabled in both directions, i.e. for adding new information about person or publication and for making query to find peers.
Further development plans adding automatic metadata extraction servers to improve quantity and quality of data or to extract further information (FixRep, paperBase).


What programming languages we use and why we love it/them  -technologies, standards, frameworks that make our lives easier (or harder).

In actual fact there are rather a lot of these! In the case of writeslike.us we have stuck to scripting languages, in particular to Perl and Python. Each of these have their benefits and their issues. Arguments centre around Python’s semantic whitespace versus Perl’s line-noise pseudo-ppp transmission ‘write-once, read never’ look, for example. However, both come with a great variety of extensions and libraries. The ‘killer app’ for Python was NLTK, and once one is used to Perl’s CPAN, it becomes indispensable for certain tasks. In the end, arguing about which language is better is pointless, even though it is great fun. The Computer Science department presently teaches Python, and as such Python is the language with which most CS students are more familiar, whilst EE students seem to be either Perl or Matlab according to recent evidence.

In the end, the important point is that prototypes are developed quickly and easily, and that the techniques and datasets underlying them are well understood. If this is the case, then the rest can usually be adapted to suit – rapid development is not the same thing as throwaway prototyping, but rationalisation of software platforms and standards can very well be part of evolutionary prototype enhancement.

Day-to-day work

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1.scrum meeting + meeting minutes

  1. see the progress made by what people present – what they did yesterday, what they expect to do today, and what worked for them. Allow the manager to keep track of how the project development is progressing and how the team are performing.
  2. find and solve potential problems before they become significant or expensive!

2. collaboration on code

  1. Allows developers to learn from each others’ expertise; permits peer-review of code (extreme programming-style?) and review of functionality.
  2. A long-term goal for this approach is to encourage developers to share code, to think of it as ‘our code’ rather than ‘my code’ and to be more open to review, reuse, constructive criticism, etc.

3. moving code between machines & testing code on different workstations

  1. A single functional installation does not mean that a development project is finished, since it may be very difficult to set up on other platforms, to understand or to reuse.
  2. It should be functionally portable and include all necessary libraries, scripts, datasets and configuration to promote remote development, reuse and external contribution to the codebase.
  3. This also encourages review and testing since it tends to highlight any difficulties with installation and use of newly developed components.

Active collaboration and a flexible approach to development in particular tend to optimise productivity, in that time spent coding also has a knowledge sharing component – and there is relatively little time spent becoming familiar with code before beginning to contribute.

Writeslike.us scenarios

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Title: Looking for a supervisor for a research project
Author: Emma Tonkin and Debra Hiom

Narrative: Alice is a student at the University of Oxford. She is looking for a supervisor for her MSc level research in Information Science. She knows what sort of research area she wants to work in, and she has found several example papers of interest to her. She would like to be able to use those papers as a first step in looking for researchers working in that area who either work at her university, an affiliated institution or somewhere geographically local. She would like to get back a list of researchers, their institutional and departmental roles and their previous work and supervisory experience.

Title: Classifying events and forums by listed participants
Author: Em (adapted from Ana’s Tea For Two article, D-Lib)

Narrative: Jonathan is a researcher in evolutionary linguistics. He has become very interested in possible mathematical mechanisms for describing the nature, growth and adaption of language, as he has heard that others, such as Partha Nyogi, have done some very interesting work in this area. Unfortunately, Jonathan is not a mathematician and finds that some of the detail is hard to follow. He realises that what he really needs to do is either to go to the right sort of event or the right sort of online forum and find some people who might be interested in exploring links between his specialist area and their own. Both of these are difficult in their own ways. To go to the right sort of event would mean identifying what sort of event that would be, and he does not have enough money to go to very many. So he chooses to look up possible events and web forums, thinking that he can look through the participant lists for names that he recognises. This is greatly simplified by a system that uses information about the papers and authors that he considers most relevant; with this information it is able to parse through lists of participants in events or online communities in order to provide him with a rough classification of how relevant the group is likely to be to his ideas.

Title: Building a ‘dance card’ for an ISRC event
Author: Em

Narrative: One of the purposes of an ISRC (Information Sciences Research Council, a fictitious but plausible organisation) event is to encourage the serendipitous meeting. Rather than simply assuming that synchronicity at the coffee-table will carry the day, the ISRC decide to produce a ‘dance card’ that suggests several other individuals that you might like to meet. Whilst elements of the composition of this ‘dance card’ are resultant from program managers’ knowledge of the individual’s interests and character, the writeslike.us service can be used to quickly build some interesting (and at times amusing) meeting suggestions, based on the individuals’ papers and output, and/or on the names and ISRC-held descriptions of the projects on which the individuals work.

Title: Facilitating collaboration in a multidisciplinary research environment
Author: Em

Narrative: Ben is an anthropologist with a particular interest in the area of paleolithic archaeology. He works in the Department of Humanities. He is very interested in exploring likely patterns of migration, and particularly in the idea that this activity may have been driven by climate change. However, the Department of Humanities has limited funding for the purpose of data collection and interpretation regarding modeling of climate change, so it is not possible for him to develop a paleoclimate simulation system. Therefore he decides that it is more appropriate for him to look for other people who have other reasons to be interested in modeling of this kind, particularly during the time period in which he is interested. This is not a trivial problem for several reasons; firstly, he does not usually publish in the same area as paleoclimatologists and therefore is unlikely to make chance acquaintances. Secondly, he and they have very different ways of describing their areas of interest, and therefore there is quite a lot of interpretation required in order to ascertain that the datasets they require are (or are not) closely related.

Title: Recording collaboration; figuring out what worked best
Author: Em

Narrative: Jennifer is a program manager for the Information Sciences Research Council, a fictitious but plausible organisation that funds information sciences research in the UK. She is tasked with deciding the future direction of ISRC funding for research-related events and related online community grants in the UK. In order to facilitate the decision, she decides that it is necessary to seek some evidence able to characterise the profile of past exemplars of these events, and the current state of the online groups that they fund. Her analysis shows that certain events attract a broad and diverse set of individuals from organisations all over the UK, and give rise to unexpected and interdisciplinary collaboration, whereas certain others attract fairly closed cliques of similarly focused individuals who are also linked online by Twitter accounts and other mechanisms for informal communication. This aids her in making her eventual decision regarding which events should receive greater funding.

Welcoming Wei Jiang to writeslike.us

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A new staff member (casual staff) has just begun work, specifically on the Writeslike.us project. He is very experienced in designing and implementing web portals, familiar with machine learning concepts and enthusiastic about project research area – constructing a graph of relations between researchers based on analysis of their papers.

Here is his home page

http://wei-jiang.com