Language-integrated provenance by trace analysis

Language-integrated provenance builds on language-integrated query techniques to make provenance information explaining query results readily available to programmers. In previous work we have explored language-integrated approaches to provenance in Links and Haskell. However, implementing a new form of provenance in a language-integrated way is still a major challenge. We propose a self-tracing transformation and trace analysis features that, together with existing techniques for type-directed generic programming, make it possible to define different forms of provenance as user code. We present our design as an extension to a core language for Links called LinksT, give examples showing its capabilities, and outline its metatheory and key correctness properties.Comment: DBPL 201

Language-integrated provenance in Links

Today’s programming languages provide no support for data prove-nance. In a world that increasingly relies on data, we need prove-nance to judge the reliability of data and therefore should aim for making it easily accessible to programmers. We report our work in progress on an extension to the Links programming language that builds on its support for language-integrated query to support where-provenance queries through query rewriting and a type system extension that distinguishes provenance metadata from other data. Our approach aims to work solely within the language implementa-tion and thus require no changes to the database system. The type system together with automatic propagation of provenance metadata will prevent programmers from accidentally changing provenance, losing it, or misattributing it to other data. 1

Language-integrated provenance by trace analysis

Language-integrated provenance builds on language-integrated query techniques to make provenance information explaining query results readily available to programmers. In previous work we have explored language-integrated approaches to provenance in Links and Haskell. However, implementing a new form of provenance in a language-integrated way is still a major challenge. We propose a self-tracing transformation and trace analysis features that, together with existing techniques for type-directed generic programming, make it possible to define different forms of provenance as user code. We present our design as an extension to a core language for Links called LinksT, give examples showing its capabilities, and outline its metatheory and key correctness properties.Comment: DBPL 201

Language-integrated provenance in Haskell

Scientific progress increasingly depends on data management, particularly to clean and curate data so that it can be systematically analyzed and reused. A wealth of techniques for managing and curating data (and its provenance) have been proposed, largely in the database community. In particular, a number of influential papers have proposed collecting provenance information explaining where a piece of data was copied from, or what other records were used to derive it. Most of these techniques, however, exist only as research prototypes and are not available in mainstream database systems. This means scientists must either implement such techniques themselves or (all too often) go without. This is essentially a code reuse problem: provenance techniques currently cannot be implemented reusably, only as ad hoc, usually unmaintained extensions to standard databases. An alternative, relatively unexplored approach is to support such techniques at a higher abstraction level, using metaprogramming or reflection techniques. Can advanced programming techniques make it easier to transfer provenance research results into practice? We build on a recent approach called language-integrated provenance, which extends language-integrated query techniques with source-to-source query translations that record provenance. In previous work, a proof of concept was developed in a research programming language called Links, which supports sophisticated Web and database programming. In this paper, we show how to adapt this approach to work in Haskell building on top of the Database-Supported Haskell (DSH) library. Even though it seemed clear in principle that Haskell's rich programming features ought to be sufficient, implementing language-integrated provenance in Haskell required overcoming a number of technical challenges due to interactions between these capabilities. Our implementation serves as a proof of concept showing how this combination of metaprogramming features can, for the first time, make data provenance facilities available to programmers as a library in a widely-used, general-purpose language. In our work we were successful in implementing forms of provenance known as where-provenance and lineage. We have tested our implementation using a simple database and query set and established that the resulting queries are executed correctly on the database. Our implementation is publicly available on GitHub. Our work makes provenance tracking available to users of DSH at little cost. Although Haskell is not widely used for scientific database development, our work suggests which languages features are necessary to support provenance as library. We also highlight how combining Haskell's advanced type programming features can lead to unexpected complications, which may motivate further research into type system expressiveness

Curating Covid-19 Data in Links

Curated scientific databases play an important role in the scientific endeavour and support is needed for the significant effort that goes into their creation and maintenance. This demonstration and case study illustrate how curation support has been developed in the Links cross-tier programming language, a functional, strongly typed language with language-integrated query and support for temporal databases. The chosen case study uses weekly released Covid-19 fatality figures from the Scottish government which exhibit updates to previously released data. This data allows the capture and query of update provenance in our prototype. This demonstration will highlight the potential for language-integrated support for curation to simplify and streamline prototyping of web-applications in support of scientific database

Using Links to prototype a Database Wiki

Both relational databases and wikis have strengths that make them attractive for use in collaborative applications. In the last decade, database-backed Web applications have been used extensively to develop valuable shared biological references called curated databases. Databases offer many advantages such as scalability, query optimization and concurrency control, but are not easy to use and lack other features needed for collaboration. Wikis have become very popular for early-stage biocuration projects because they are easy to use, encourage sharing and collaboration, and provide built-in support for archiving, history-tracking and annotation. However, curation projects often outgrow the limited capabilities of wikis for structuring and efficiently querying data at scale, necessitating a painful phase transition to a database-backed Web application. We perceive a need for a new class of general-purpose system, which we call a Database Wiki, that combines flexible wiki-like support for collaboration with robust database-like capabilities for structuring and querying data. This paper presents DBWiki, a design prototype for such a system written in the Web programming language Links. We present the architecture, typical use, and wiki markup language design for DBWiki and discuss features of Links that provided unique advantages for rapid Web/database application prototyping

A Linked Data Approach to Sharing Workflows and Workflow Results

A bioinformatics analysis pipeline is often highly elaborate, due to the inherent complexity of biological systems and the variety and size of datasets. A digital equivalent of the ‘Materials and Methods’ section in wet laboratory publications would be highly beneficial to bioinformatics, for evaluating evidence and examining data across related experiments, while introducing the potential to find associated resources and integrate them as data and services. We present initial steps towards preserving bioinformatics ‘materials and methods’ by exploiting the workflow paradigm for capturing the design of a data analysis pipeline, and RDF to link the workflow, its component services, run-time provenance, and a personalized biological interpretation of the results. An example shows the reproduction of the unique graph of an analysis procedure, its results, provenance, and personal interpretation of a text mining experiment. It links data from Taverna, myExperiment.org, BioCatalogue.org, and ConceptWiki.org. The approach is relatively ‘light-weight’ and unobtrusive to bioinformatics users

An Architecture for Provenance Systems

This document covers the logical and process architectures of provenance systems. The logical architecture identifies key roles and their interactions, whereas the process architecture discusses distribution and security. A fundamental aspect of our presentation is its technology-independent nature, which makes it reusable: the principles that are exposed in this document may be applied to different technologies