Provenance: The Bridge Between Experiments and Data

Current scientific applications are often structured as workflows and rely on workflow systems to compile abstract experiment designs into enactable workflows that utilise the best available resources. The automation of this step and of the workflow enactment, hides the details of how results have been produced. Knowing how compilation and enactment occurred allows results to be reconnected with the experiment design. We investigate how provenance helps scientists to connect their results with the actual execution that took place, their original experiment and its inputs and parameters.

PrIMe: A Methodology for Developing Provenance-Aware Applications

Provenance refers to the past processes that brought about a given (version of an) object, item or entity. By knowing the provenance of data, users can often better understand, trust, reproduce, and validate it. A provenance-aware application has the functionality to answer questions regarding the provenance of the data it produces, by using documentation of past processes. PrIMe is a software engineering technique for adapting application designs to enable them to interact with a provenance middleware layer, thereby making them provenance-aware. In this article, we specify the steps involved in applying PrIMe, analyse its effectiveness, and illustrate its use with two case studies, in bioinformatics and medicine.

The Open Provenance Model Core Specification (v1.1)

The Open Provenance Model is a model of provenance that is designed to meet the following requirements: (1) To allow provenance information to be exchanged between systems, by means of a compatibility layer based on a shared provenance model. (2) To allow developers to build and share tools that operate on such a provenance model. (3) To define provenance in a precise, technology-agnostic manner. (4) To support a digital representation of provenance for any 'thing', whether produced by computer systems or not. (5) To allow multiple levels of description to coexist. (6) To define a core set of rules that identify the valid inferences that can be made on provenance representation. This document contains the specification of the Open Provenance Model (v1.1) resulting from a community-effort to achieve inter-operability in the Provenance Challenge series.

Mapping Attribution Metadata to the Open Provenance Model

A description of a data item's provenance can be provided in dierent forms, and which form is best depends on the intended use of that description. Because of this, dierent communities have made quite distinct underlying assumptions in their models for electronically representing provenance. Approaches deriving from the library and archiving communities emphasise agreed vocabulary by which resources can be described and, in particular, assert their attribution (who created the resource, who modied it, where it was stored etc.) The primary purpose here is to provide intuitive metadata by which users can search for and index resources. In comparison, models for representing the results of scientific workflows have been developed with the assumption that each event or piece of intermediary data in a process' execution can and should be documented, to give a full account of the experiment undertaken. These occurrences are connected together by stating where one derived from, triggered, or otherwise caused another, and so form a causal graph. Mapping between the two approaches would be benecial in integrating systems and exploiting the strengths of each. In this paper, we specify such a mapping between Dublin Core and the Open Provenance Model. We further explain the technical issues to overcome and the rationale behind the approach, to allow the same method to apply in mapping similar schemes.

Transparent Provenance Derivation for User Decisions

It is rare for data's history to include computational processes alone. Even when software generates data, users ultimately decide to execute software procedures, choose their configuration and inputs, reconfigure, halt and restart processes, and so on. Understanding the provenance of data thus involves understanding the reasoning of users behind these decisions, but demanding that users explicitly document decisions could be intrusive if implemented naively, and impractical in some cases. In this paper, therefore, we explore an approach to transparently deriving the provenance of user decisions at query time. The user reasoning is simulated, and if the result of the simulation matches the documented decision, the simulation is taken to approximate the actual reasoning. The plausibility of this approach requires that the simulation mirror human decision -making, so we adopt an automated process explicitly modelled on human psychology. The provenance of the decision is modelled in OPM, allowing it to be queried as part of a larger provenance graph, and an OPM profile is provided to allow consistent querying of provenance across user decisions.

Automatically Adapting Source Code to Document Provenance

Being able to ask questions about the provenance of some data requires documentation on each influence on that data's existence and content. Much software exists, and is being developed, for which there is no provenance-awareness, i.e. at best, the data it outputs can be connected to its inputs, but with no record of intermediate processing. Further, where some record of processing does exist, e.g. as logs, it is not in a form easily connected with that of other processes. We would like to enable compiled software to record useful documentation without requiring prior manual adaptation. In this paper, we present an approach to adapting source code from its original form without manual manipulation, to record information on data provenance during execution.

Requirements for Provenance on the Web

From where did this tweet originate? Was this quote from the New York Times modified? Daily, we rely on data from the Web but often it is difficult or impossible to determine where it came from or how it was produced. This lack of provenance is particularly evident when people and systems deal with Web information or with any environment where information comes from sources of varying quality. Provenance is not captured pervasively in information systems. There are major technical, social, and economic impediments that stand in the way of using provenance effectively. This paper synthesizes requirements for provenance on the Web for a number of dimensions focusing on three key aspects of provenance: the content of provenance, the management of provenance records, and the uses of provenance information. To illustrate these requirements, we use three synthesized scenarios that encompass provenance problems faced by Web users today.

Genetic Variation in an International Provenance-Progeny Test of Pinus caribaea Mor. var. bahamensis Bar. et Gol., in São Paulo, Brazil

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

U-Pb geochronology of the southern Brasília belt (SE-Brazil): Sedimentary provenance, Neoproterozoic orogeny and assembly of West Gondwana

The Brasília belt borders the western margin of the São Francisco Craton and records the history of ocean opening and closing related to the formation of West Gondwana. This study reports new U-Pb data from the southern sector of the belt in order to provide temporal limits for the deposition and ages of provenance of sediments accumulated in passive margin successions around the south and southwestern margins of the São Francisco Craton, and date the orogenic events leading to the amalgamation of West Gondwana. Ages of detrital zircons (by ID-TIMS and LA-MC-ICPMS) were obtained from metasedimentary units of the passive margin of the São Francisco Craton from the main tectonic domains of the belt: the internal allochthons (Araxá Group in the Áraxá and Passos Nappes), the external allochthons (Canastra Group, Serra da Boa Esperança Metasedimentary Sequence and Andrelândia Group) and the autochthonous or Cratonic Domain (Andrelândia Group). The patterns of provenance ages for these units are uniform and are characterised as follows: Archean- Paleoproterozoic ages (3.4-3.3, 3.1-2.7, and 2.5-2.4Ga); Paleoproterozoic ages attributed to the Transamazonian event (2.3-1.9Ga, with a peak at ca. 2.15Ga) and to the ca. 1.75Ga Espinhaço rifting of the São Francisco Craton; ages between 1.6 and 1.2Ga, with a peak at 1.3Ga, revealing an unexpected variety of Mesoproterozoic sources, still undetected in the São Francisco Craton; and ages between 0.9 and 1.0Ga related to the rifting event that led to the individualisation of the São Francisco paleo-continent and formation of its passive margins. An amphibolite intercalation in the Araxá Group yields a rutile age of ca. 0.9Ga and documents the occurrence of mafic magmatism coeval with sedimentation in the marginal basin. Detrital zircons from the autochthonous and parautochthonous Andrelândia Group, deposited on the southern margin of the São Francisco Craton, yielded a provenance pattern similar to that of the allochthonous units. This result implies that 1.6-1.2Ga source rocks must be present in the São Francisco Craton. They could be located either in the cratonic area, which is mostly covered by the Neoproterozoic epicontinental deposits of the Bambuí Group, or in the outer paleo-continental margin, buried under the allochthonous units of the Brasília belt. Crustal melting and generation of syntectonic crustal granites and migmatisation at ca. 630Ma mark the orogenic event that started with westward subduction of the São Francisco plate and ended with continental collision against the Paraná block (and Goiás terrane). Continuing collision led to the exhumation and cooling of the Araxá and Passos metamorphic nappes, as indicated by monazite ages of ca. 605Ma and mark the final stages of tectonometamorphic activity in the southern Brasília belt. Whilst continent-continent collision was proceeding on the western margin of the São Francisco Craton along the southern Brasília belt, eastward subduction in the East was generating the 634-599Ma Rio Negro magmatic arc which collided with the eastern São Francisco margin at 595-560Ma, much later than in the Brasília belt. Thus, the tectonic effects of the Ribeira belt reached the southernmost sector of the Brasília belt creating a zone of superposition. The thermal front of this event affected the proximal Andrelândia Group at ca. 588Ma, as indicated by monazite age. The participation of the Amazonian craton in the assembly of western Gondwana occurred at 545-500Ma in the Paraguay belt and ca. 500Ma in the Araguaia belt. This, together with the results presented in this work lead to the conclusion that the collision between the Paraná block and Goiás terrane with the São Francisco Craton along the Brasília belt preceded the accretion of the Amazonian craton by 50-100 million years. © 2003 Elsevier B.V. All rights reserved.

Intraspecific variability of Holostylis reniformis: concentration of lignans, as determined by maceration and supercritical fluid extraction (SFE-CO2), as a function of plant provenance and plant parts

Maceration and supercritical fluid extraction were used to prepare extracts from parts of plants (Holostylis reniformis) collected in two different regions of Brazil. ¹H NMR, HPLC-DAD-ESI/MS, HPLC-DAD, GC-MS, and chemometric techniques were used to analyse lignans in the extracts and showed that yields of SFE-CO2 were less than or equal to those of hexane maceration extracts. These analyses, in conjunction with the concentrations of aliphatic hydrocarbons, fatty acids and their methyl and ethyl derivatives in the extracts, also allowed the chemical composition of parts and provenance of the plant to be differentiated.

Sedimentological and provenance response to Cambrian closure of the Clymene ocean: The upper Alto Paraguai Group, Paraguay belt, Brazil

Final Gondwana amalgamation was marked by the closure of the Neoproterozoic Clymene ocean between the Amazonia craton and central Gondwana. The events which occurred in the last stage of this closure were recorded in the upper Alto Paraguai Group in the foreland of the Paraguay orogen. Outcrop-based fades analysis of the siliciclastic rocks of upper Alto Paraguai Group, composed of the Sepotuba and Diamantino Formations, was carried out in the Diamantino region, within the eastern part of the Barra dos Bugres basin, Mato Grosso state, central-western Brazil. The Sepotuba Formation is composed of sandy shales with planar to wave lamination interbedded with fine-grained sandstone with climbing ripple cross-lamination, planar lamination, swaley cross-stratification and tangential to sigmoidal cross-bedding with mud drapes, related to marine offshore deposits. The lower Diamantino Formation is composed of a monotonous, laterally continuous for hundreds of metres, interbedded siltstone and fine-grained sandstone succession with regular parallel lamination, climbing ripple cross-lamination and ripple-bedding interpreted as distal turbidites. The upper part of this formation consists of fine to medium-grained sandstones with sigmoidal cross-bedding, planar lamination, climbing ripple cross-lamination, symmetrical to asymmetrical and linguoid ripple marks arranged in lobate sand bodies. These fades are interbedded with thick siltstone in coarsening upward large-scale cycles related to a delta system. The Sepotuba Formation characterises the last transgressive deposits of the Paraguay basin representing the final stage of a marine incursion of the Clymene ocean. The progression of orogenesis in the hinterland resulted in the confinement of the Sepotuba sea as a foredeep sub-basin against the edge of the Amazon craton. Turbidites were generated during the deepening of the basin. The successive filling of the basin was associated with progradation of deltaic lobes from the southeast, in a wide lake or a restricted sea that formed after 541 +/- 7 Ma. Southeastern to east dominant Neoproterozoic source regions were confirmed by zircon grains that yielded ages around 600 to 540 Ma, that are interpreted to be from granites in the Paraguay orogen. This overall regressive succession recorded in the Alto Paraguai Group represents the filling up of a foredeep basin after the final amalgamation of westem Gondwana in the earliest Phanerozoic. (C) 2011 International Association for Gondwana Research. Published by Elsevier B.V. All rights reserved.

Depositional age, provenance and metamorphic age of metasedimentary rocks from southern Madagascar

Southern Madagascar is the core of a >1 million km(2) Gondwanan metasedimentary belt that forms much of the southern East African Orogen of eastern Africa, Madagascar, southern India and Sri Lanka. Here the Vohibory Series yielded U-Pb isotopic data from detrital zircon cores that indicate that it was deposited in the latest Tonian to late Cryogenian (between -900 and 640 Ma). The deposition of the Graphite and Androyen Series protoliths is poorly constrained to between the late Palaeoproterozoic and the Cambrian (similar to 1830-530 Ma). The Vohibory Series protoliths were sourced from very restricted-aged sources with a maximum age range between 910 and 760 Ma. The Androyen and Graphite Series protoliths were sourced from Palaeoproterozoic rocks ranging in age between 2300 and 1800 Ma. The best evidence of the timing of metamorphism in the Vohibory Series is a weighted mean Pb-206/U-238 age of 642 +/- 8 Ma from 3 analyses of zircon from sample M03-01. A considerably younger Pb-206/U-238 metamorphic age of 531 +/- 7 Ma is produced from 10 analyses of zircon from sample M03-28 in the Androyen Series. This similar to 110 Ma difference in age is correlated with the early East African Orogeny affecting the west of Madagascar along with its type area in East Africa, whereas the Cambrian Malagasy Orogeny affected the east of Madagascar and southern India during the final suturing of the Mozambique Ocean. (C) 2011 International Association for Gondwana Research. Published by Elsevier B.V. All rights reserved.

Neoproterozoic glacial deposits from the Aracuai orogen, Brazil: Age, provenance and correlations with the Sao Francisco craton and West Congo belt

Glacigenic diamictite successions of the Macaubas Group are widespread in the western domain of the Aracuai orogen, east of the Sao Francisco craton (Brazil). Diamictites also occur on this craton and in the African counterpart of the Aracuai orogen, the West Congo belt. Detrital zircon grains from the matrix of diamictites and sandstones from the Macaubas Group were dated by the U-Pb SHRIMP technique. The geochronological study sets the maximum depositional age of the glacial diamictites at 900 Ma, and indicates multiple sources for the Macaubas basin with ages ranging from 900 to 2800 Ma. Sm-Nd T-DM model ages, determined on whole rock samples, range from 1.8 Ga to 2.5 Ga and get older up-section. Comparison of our data with those from the cratonic area suggest that these glacial deposits can be correlated to the Jequitai and Carrancas diamictites in the Sao Francisco craton, and to the Lower Mixtite Formation of the West Congolian Group, exposed in Africa. The 900-1000 Ma source is most probably represented by the Zadinian-Mayumbian volcanic rocks and related granites from the West Congo belt. However, one of the most voluminous sources, with ages in the 1.1-1.3 Ga interval, has not been detected in the Sao Francisco-Congo craton. Possible sources for these grains could occur elsewhere in Africa, or possibly from within the Brasilia Belt in western central Brazil. (C) 2011 International Association for Gondwana Research. Published by Elsevier B.V. All rights reserved.