Articles | Volume 14, issue 11
Geosci. Model Dev., 14, 6711–6740, 2021
https://doi.org/10.5194/gmd-14-6711-2021

Special issue: The Loop 3D stochastic geological modelling platform – development...

Geosci. Model Dev., 14, 6711–6740, 2021
https://doi.org/10.5194/gmd-14-6711-2021

Development and technical paper 04 Nov 2021

Development and technical paper | 04 Nov 2021

dh2loop 1.0: an open-source Python library for automated processing and classification of geological logs

dh2loop 1.0: an open-source Python library for automated processing and classification of geological logs
Ranee Joshi1, Kavitha Madaiah1, Mark Jessell1, Mark Lindsay1,2, and Guillaume Pirot1 Ranee Joshi et al.
  • 1Mineral Exploration Cooperative Research Centre, Centre for Exploration Targeting, School of Earth Sciences, The University of Western Australia, Perth, Australia
  • 2CSIRO Mineral Resources, CSIRO - Kensington, Australian Resources Research Centre (ARRC), Kensington, Australia

Correspondence: Ranee Joshi (ranee.joshi@research.uwa.edu.au)

Abstract

A huge amount of legacy drilling data is available in geological survey but cannot be used directly as they are compiled and recorded in an unstructured textual form and using different formats depending on the database structure, company, logging geologist, investigation method, investigated materials and/or drilling campaign. They are subjective and plagued by uncertainty as they are likely to have been conducted by tens to hundreds of geologists, all of whom would have their own personal biases. dh2loop (https://github.com/Loop3D/dh2loop, last access: 30 September 2021​​​​​​​) is an open-source Python library for extracting and standardizing geologic drill hole data and exporting them into readily importable interval tables (collar, survey, lithology). In this contribution, we extract, process and classify lithological logs from the Geological Survey of Western Australia (GSWA) Mineral Exploration Reports (WAMEX) database in the Yalgoo–Singleton greenstone belt (YSGB) region. The contribution also addresses the subjective nature and variability of the nomenclature of lithological descriptions within and across different drilling campaigns by using thesauri and fuzzy string matching. For this study case, 86 % of the extracted lithology data is successfully matched to lithologies in the thesauri. Since this process can be tedious, we attempted to test the string matching with the comments, which resulted in a matching rate of 16 % (7870 successfully matched records out of 47 823 records). The standardized lithological data are then classified into multi-level groupings that can be used to systematically upscale and downscale drill hole data inputs for multiscale 3D geological modelling. dh2loop formats legacy data bridging the gap between utilization and maximization of legacy drill hole data and drill hole analysis functionalities available in existing Python libraries (lasio, welly, striplog).

1 Introduction

Drilling is a process of penetrating through the ground that is capable of extracting information about rocks from various depths below the surface. This is useful for establishing the geology beneath the surface. Drill core or cuttings can be collected, thus providing samples for description, interpretation and analysis. The location of where drilling starts is referred to as the collar. As the drilling progresses, survey orientation measurements are taken to be able to convert the specific depths to exact coordinate locations of the drill core being retrieved. In a hard-rock setting, geological drill core logging is the process whereby the recovered drill core sample is systematically studied to determine the lithology, mineralization, structures and alteration zones of a potential mineral deposit. It is usually performed by geologists who classify a rock unit into a code, based on one or multiple properties such as rock type, alteration intensity and mineralization content. Exploration and mining companies rely on the diverse geoscientific information obtained by drill core logging techniques to target and to build models for prospectivity mapping or mine planning. This work focuses on lithological logs, which are the component of a geological log that refers to the geological information on the dominant rock type in a specific downhole interval. Inevitably, lithological drill core logging is subjective and plagued by uncertainty as all logging geologists have their own personal biases (Lark et al., 2014). The information and level of detail contained in logs are highly dependent on the purpose of the study; this already makes geological logging subjective. This subjectivity is also influenced by the lack of a standard between projects and/or companies combined with the personal biases of the logging geologist. Furthermore, it can be difficult to recognize lithology with confidence and to establish subtle variations or boundaries in apparently homogeneous sequences.

With the advent of the digital age, semi-automated drill core logging techniques such as X-ray diffraction (XRD), X-ray fluorescence spectrometry (XRF) and hyperspectral (HS) imaging have provided higher detail of data collection and other properties such as conductivity, volumetric magnetic susceptibility, density using gamma-ray attenuation and chemical elements during logging (Zhou et al., 2003; Rothwell and Rack, 2006; Ross et al., 2013). This has prompted a shift towards using numerical data rather than depending on traditional geological drill core logging procedures (Culshaw, 2005). Multiple methods have been recently applied to geological drill core logging such as wavelet transform analysis or data mosaic (Arabjamaloei et al., 2011; Hill et al., 2020; Le Vaillant et al., 2017; Hill et al., 2015), an artificial neural network model (Lindsay, 2019; Zhou et al., 2019; Emelyanova et al., 2017), and inversion (Zhu et al., 2019). Relying solely on these semi-automatic methods comes with drawbacks as it excludes some of the subjective interpretations that cannot be replaced. The semi-automatic methods are also poor at describing textural characteristics (foliation, banding, grain size variation). Furthermore, a rich amount of legacy data is collected in the traditional drill core logging method, and disregarding this information limits the dataset.

Legacy data are information collected, compiled and/or stored in the past in many different old or obsolete formats or systems, such as handwritten records, aperture cards, floppy disks, microfiche, transparencies, magnetic tapes and/or newspaper clippings, making it difficult to access and/or process them (Smith et al., 2015). Legacy digital data also suffer from a lack of standardization and inconsistency. In geoscience, these are currently scattered amongst unpublished company reports, departmental reports, publications, petrographic reports, printed plans and maps, aerial photographs, field notebooks, sample ticket books, drill core samples, tenement information, and geospatial data, providing a major impediment to their efficient use. This includes geological drill core logs that are the outcome of most expensive part of mineral exploration campaigns: drilling. This is a valuable information source and a key asset that can be used to add value to geoscientific data for research and exploration, design mapping programs and research questions of interest, more efficiently target remapping and sustainable new discoveries, and provide customers with all existing information at the start of the remapping program. Legacy drilling data should not to be abandoned even though (1) their recovery and translation into a digital format is tedious and (2) they may have lower intrinsic quality than observations made with more modern equipment. Griffin (2015) argues that there is no distinction in principle between legacy data and “new” data, as all of it is data. The intention of recovering legacy data is to (a) upcycle information with integration into modern datasets, (b) use salvaged data for new scientific applications and (c) allow re-use of that information into utility downstream applications (Vearncombe et al., 2017). Furthermore, extracting information from legacy datasets is valuable and relatively low-risk as geoscientific insight is added to a project at little or no cost compared to that of drilling (Vearncombe et al., 2016).

The primary challenge in dealing with geological legacy datasets is that a large amount of important data, information and knowledge are recorded in an unstructured textural form, such as host rock, alteration types, geological setting, ore-controlled factors, geochemical and geophysical anomaly patterns, and location (Wang and Ma, 2019). To acknowledge the ambiguity of “unstructured textual form”, we define it in this paper as “descriptive text that lacks a pre-defined format and/or metadata and thus cannot be readily indexed and mapped into standard database fields”. The geological drill core logging forms and formats also vary depending on the company, logging geologist, investigation method, investigated materials and/or drilling campaign. Natural language processing (NLP), also known as computational linguistics, has been used for information extraction, text classification and automatic text summarization (Otter et al., 2020). NLP applications on legacy data have been demonstrated in the fields of taxonomy (Rivera-Quiroz and Miller, 2019), biomedicine (Liu et al., 2011) and legal services (Jallan et al., 2019). Qiu et al. (2020) proposed an ontology-based methodology to support automated classification of geological reports using word embeddings, geoscience dictionary matching and a bidirectional long short-term memory model (Dic-Att-BiLSTM) that assists in identifying the difference in relevance from a report. Padarian and Fuentes (2019) also introduced the use of domain-specific word embeddings (GeoVec) which are used to automate and reduce subjectivity of geological mapping of drill hole descriptions (Fuentes et al., 2020).

Similarity matching has many applications in natural language processing as it is one of the best techniques for improving retrieval effectiveness (Park et al., 2005). The use of text similarity is beneficial for text categorization (Liu and Guo, 2005) and text summarization (Erkan and Radev, 2004; Lin and Hovy, 2003). It has been used to extract lithostratigraphic markers from drill lithology logs (Schetselaar and Lemieux, 2012). Fuzzy string matching, also known as approximate string matching, is the process of finding strings that approximately match a given pattern (Cohen, 2011; Gonzalez et al., 2017). It has been used in language syntax checker, spell-checking, DNA analysis and detection, spam detection, sport and concert event ticket search (Higgins and Mehta, 2018), text re-use detection (Recasens et al., 2013), and clinical trials (Kumari et al., 2020).

Most of the available Python libraries have been built to process extracted and standardized drill hole data. The most common of these are lasio (https://lasio.readthedocs.io/en/latest/, last access: 30 September 2021​​​​​​​), which deals with reading and writing Log ASCII Standard (LAS) files, a drill hole format commonly used in the oil and gas industry, welly (https://github.com/agile-geoscience/welly, last access: 30 September 2021), which deals with loading, processing and analysis of drill holes, and striplog (https://github.com/agile-geoscience/striplog, last access: 30 September 2021), which digitizes, visualizes and archives stratigraphic and lithological data. striplog (Hall and Keppie, 2016) also parses natural language “descriptions”, converting them into structured data via an arbitrary lexicon which allows further querying and analysis on drill hole data. The main limitation of these existing libraries, with respect to legacy data in the mining sector, is that they assume that the data are already standardized and pre-processed.

dh2loop provides the functionality to extract and standardize geologic drill hole data and export them into readily importable interval tables (collar, survey, lithology). It addresses the subjective nature and variability of the nomenclature of lithological descriptions within and across different drilling campaigns by integrating published dictionaries, glossaries and/or thesauri that are built to improve the resolution of poorly defined or highly subjective use of terminology and idiosyncratic logging methods. It is, however, important to highlight that verifying the accuracy and/or correctness of the geological logs being standardized is outside the scope of this tool; thus we assume logging has been conducted to the best of the geologist's ability.

Furthermore, it classifies lithological data into multi-level groupings that can be used to systematically upscale and downscale drill hole data inputs in a multiscale 3D geological model. It also provides drill hole de-surveying (computes the geometry of a drill hole in three-dimensional space) and log correlation functions so that the results can be plotted in 3D and analysed against each other. It also links the gap between utilization and maximization of legacy drill hole data and the drill hole analysis functionalities available in existing Python libraries.

2dh2loop drill hole data extraction

2.1 Conventions and terminologies

This paper involves multiple Python libraries, database tables and fields (Appendix A1). For clarity, the following conventions are used for this paper:

  1. Python libraries are written in italics: dh2loop

  2. Python functions are written in italics followed by an open and close parenthesis: token_set_ratio()

  3. Database tables are written in italic typewriter font: dhgeology

  4. Database table fields are written in roman typewriter font: CollarID

  5. Workflows are written in bold: Lithology Code workflow

2.2 Data source

The Geological Survey of Western Australia (GSWA) Mineral Exploration Reports Database (WAMEX) contains open-file reports submitted as a compliance to the Sunset Clause, Regulation 96(4) of the Western Australia legislation Mining Regulations 1981. These reports contain valuable exploration information in hard copy (1957–2000), hard copy, and digital format (2000–2007) and digital format (2000–present) (Riganti et al., 2015). The minimum contents of a drilling report comprise a collar file, which describes the geographic coordinates of the collar location (Fig. B1). Additional files may be included, such as a survey file describing the depth, azimuth and inclination measurements for the drilling path; assays, downhole geology and property surveys (e.g. downhole geochemistry, petrophysics) may also be available depending on the company's submission (Riganti et al., 2015). The data in the drilling reports are extracted with spatial attribution and imported to a custom-designed relational database (also called the Mineral Drill hole Database) curated by the GSWA that allows easy retrieval and spatial querying. For simplicity, we will refer to this database as the WAMEX database in this text.

The WAMEX database contains more than 50 years' worth of mineral exploration drill hole data with more than 2.05 million drill holes, imported from over 1514 companies. Each drill hole is identified by its surface coordinates and its unique ID (CollarID) in the collar table (Fig. B1). The drill hole 3D geometry is described in the survey tables (dhsurvey, dhsurveyattr). The lithology along the drill hole is described as a function of depth in the lithology tables (dhgeology and dhgeologyattr). However, it is important to emphasize that the drill hole data are of variable quality and reliability and that no validation has been done. The necessary amendments and reformatting enabling us to extract and utilize data from the WAMEX database are part of the functionalities provided by dh2loop.

2.3 Thesauri

Since most exploration companies have their own nomenclature and systems, which could also change between drilling campaigns, it is necessary to build thesauri: dictionaries that list equivalent and related nomenclature (or synonyms) for different attribute names and values. Synonyms include terms that share a similar intent, for example, RL (relative level) terms, whether elevation or relative level, as long as the words record a vertical height. These thesauri are stored as additional tables in the database. For example, if we are interested in the major lithology in a specific interval, this information can be tabulated as “Major Rock Type”, “Lithology_A” or “Main_Geology_Unit” depending on the drill core logging system used. The resulting thesauri considers change in cases, abbreviations, the addition of characters, typographical errors and a combination of these. Although listing out these terms is manual and tedious, it only needs to be done once and can be re-used and forms the basis for future text matching and as a training set to automate finding similar terms. This is preferred over selection based on regular expressions as when parsing these terms, there are complex patterns in the terms used and inconsistencies in the way they are written that can be understood by a person with a geological background but not by a simple regular expression. The complexity of the regular expression required to catch all the terms of interest means an optimal expression is difficult, if not impossible, to define and also tends to be computationally burdensome. dh2loop provides several thesauri that can easily be updated (if needed) for the following attributes (Appendix A1). In order to extract the other attributes, we envisage developing other thesauri, following the same workflow.

  1. Drill Hole Collar Elevation Thesaurus: 360 synonyms such as “elevation” and “relative level”.

  2. Drill Hole Maximum Depth Thesaurus: 160 synonyms such as “end of hole”, “final depth” and “total depth”.

  3. Drill Hole Survey Azimuth Thesaurus: 142 synonyms.

  4. Drill Hole Survey Inclination Thesaurus: 8 synonyms such as “dip”.

  5. Drill Hole Lithology Thesaurus: 688 synonyms such as “geology”, “Lithology_A”, “Major_Geology_Unit” and “Major_ Rock_Type”.

  6. Drill Hole Comments Thesaurus: 434 synonyms such as “description”.

The thesauri created specifically for further processing lithology and comment information are the following:

  • 7.

    Drill Hole Lithology Codes Thesaurus: it compiles the equivalent lithology for a given lithological code based on the reports submitted to GSWA. This thesaurus is identified by a company ID and report number.

  • 8.

    Clean-up Dictionary: it is a list of words and non-alphabetic characters that are used as descriptions in the geological logging syntax. This dictionary is used to remove these terms from the Company_Litho and/or Comments free-text descriptions prior to the fuzzy string matching. The dictionary is composed of terms that describe age, location, structural forms, textures, amount or distribution, minerals, colours, symbols and common phrases, compiled from abbreviations in field and mine geological mapping (Chace, 1956) and the CGI-IUGS (International Union of Geological Sciences Commission for the Management and Application of Geoscience Information) geoscience vocabularies accessible at http://geosciml.org/resource/def/voc/ (last access: 30 September 2021)​​​​​​​ (Simons et al., 2006; Richard and CGI Interoperability Working Group, 2007; Raymond et al., 2012).

  • 9.

    Lithology Hierarchical Thesaurus: it is a list of 757 rock names (Detailed_Lithology), their synonyms and a two-level upscale grouping (Lithology_Subgroup and Lithology_Group) (Fig. 1). Each row in Detailed_Lithology refers to a rock name. Each rock name row lists the standardized terminology first, followed by its synonyms. The two corresponding columns for this row indicated the two-level upscale grouping. Many of the Lithology_Subgroups listed have parent–child relationships e.g. “mafic_fine_grained_ crystalline” is a child of “mafic”. Parents in parent–child relationships are included in their children as catch-all groups to capture free-text descriptions that do not include details that would be captured by only using the child terms alone. In total, 169 of these rock names are compiled from the CGI-IUGS Simple Lithology vocabulary available at http://resource.geosciml.org/classifier/cgi/lithology (last access: 30 September 2021) (Simons et al., 2006; Richard and CGI Interoperability Working Group, 2007; Raymond et al., 2012). The synonyms are obtained from https://mindat.org (last access: 30 September 2021) (Ralph, 2021). The hierarchical classification is inherited from both https://mindat.org (Ralph, 2021) and the British Geological Survey (BGS) Classification Scheme (Gillespie and Styles, 1999; Robertson, 1999; Hallsworth and Knox, 1999; McMillan and Powell, 1999; Rosenbaum et al., 2003). It is important to use multiple libraries to be able to build an exhaustive thesaurus as some libraries are limited by the nomenclature, level of interest, and presence of the lithology or rock group in a geographic area. For example, the BGS classification did not have a comprehensive regolith dictionary. Thus, regolith has been classified using the regolith glossary (Eggleton, 2001).

https://gmd.copernicus.org/articles/14/6711/2021/gmd-14-6711-2021-f01

Figure 1Lithology Hierarchical Thesaurus showing the seven major Lithology_Groups: igneous rocks (pink), sedimentary rocks (light brown), metamorphic rocks (green), surficial rocks (light yellow), texture and structure (blue), mineralization (purple) and unclassified rocks (dark yellow) and their corresponding Lithology_Subgrouups.

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2.4 Data extraction

Currently, the dh2loop library extracts collar, survey and lithology information. The paper focuses on the lithological extraction. Database structure and extraction results for collar and survey are available in Appendices B3 and B4. The extraction uses a configuration file that allows the user to define the inputs, which are as follows:

  1. region of interest (in WGS (World Geodetic System) 1984 lat/long) and/or

  2. list of drill hole ID codes if known

  3. if reprojection is desired, the EPSG (European Petroleum Survey Group) code of the projected coordinate system (e.g. EPSG:28350 for MGA (Map Grid of Australia) Zone 50; http://epsg.io, last access: 30 September 2021​​​​​​​)

  4. the connection credentials to the local copy of the WAMEX database

  5. input and output file directories/location.

The lithology extraction is divided into two workflows: Lithology Code workflow and Comments workflow. Both workflows output a lithology CSV file containing the following information (Fig. 2):

  1. CompanyID: the primary key to link the lithology code to the Drill Hole Lithology Codes Thesaurus and decode the lithologies.

  2. CollarID: the primary key to link the lithology information to the collar file.

  3. FromDepth and ToDepth: if the ToDepth is null, we assume ToDepth to be equal to FromDepth+ 0.01. If the FromDepth is larger than ToDepth, the FromDepth and ToDepth values are switched.

  4. Detailed_Lithology: this value is the lithology matched through fuzzy string matching. The string that serves as input to the fuzzy string matching may either be the Company_Litho (decoded lithology from Company_LithoCode) or from the Comments (free-text descriptions).

    • 4.1.

      Decoding Lithological Codes

      • 4.1.1.

        Company_LithoCode: this fetches the lithology codes that are typically three-letter codes using the Drill Hole Lithology Thesaurus.

      • 4.1.2.

        Company_Litho: the Company_Litho is fetched by matching the CompanyID and Company_LithoCode to the Drill Hole Lithology Codes Thesaurus.

    • 4.2.

      Comments: this fetches the free-text descriptions using the Drill Hole Comments Thesaurus.

  5. Lithology_Subgroup and Lithology_Group: upscales the lithological information to more generic rock groups. For example, Detailed_Lithology: “basalt” is upscaled to Lithology_Subgroup: “mafic_fine-grained crystalline” and further upscaled to Lithology_Group: “igneous rock”.

  6. calculated X, Y, Z for the start, mid- and endpoint also using the minimum curvature algorithm. The de-surveying code is heavily based on the pyGSLIB drill hole module.

https://gmd.copernicus.org/articles/14/6711/2021/gmd-14-6711-2021-f02

Figure 2Lithology extraction is done through the Lithology Code workflow and Comments workflow. The values are fetched from the dhgeology and dhgeologyattr table (green) using either the Drill Hole Lithology Thesaurus (blue) and Drill Hole Lithology Codes Thesaurus (light blue) or the Drill Hole Comments Thesaurus (blue). The string fetched is then cleaned prior to the fuzzy string matching using the Clean-up Dictionary (dark yellow). The result is then matched against the Detailed_Lithology level of the Lithological Hierarchical Thesaurus. If there is a match with a score greater or equal to 80, the match is taken and matched with the rest of the columns in the Lithology Hierarchical Thesaurus. If not, it is labelled as unclassified rock.

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Once the Company_Litho (decoded lithology from Company_LithoCode or from the Comments (free-text descriptions) has been extracted from the database, the lithology strings are pre-processed such that

  • a.

    the strings are converted to lowercase form;

  • b.

    the strings inside parenthesis, brackets and braces are removed, as these are found to reduce the accuracy of the matching;

  • c.

    the strings preceded by key phrases such as “with”, “possibly” and “similar to” are removed;

  • d.

    if any of the words listed in the Clean-up Dictionary are present in the string, these words are removed;

  • e.

    lemmatization, the removal of the inflections at the end of the words in order to obtain the “lemma” or root of the words, is applied to all nouns (Müller et al., 2015);

  • f.

    all words with non-alphabetic characters and tokens with less than three characters are removed; this includes two-letter words such as “to”, “in” and “at”;

  • g.

    stopwords, a set of words frequently used in language which are irrelevant for text mining purposes (Wilbur and Sirotkin, 1992), are removed. Examples of stopwords are as follows: “as”, “the”, “is”, “at”, “which” and “on”.

This is followed by fuzzy string matching, a technique that finds the string that matches a pattern approximately. Fuzzy string matching is typically divided into two sub-problems: (1) finding approximate substring matches inside a given string and (2) finding dictionary strings that match the pattern approximately. Fuzzy string matching uses the Levenshtein distance to calculate the differences between sequences and patterns (Okuda et al., 1976; Cohen, 2011). The Levenshtein distance measures the minimum number of single-character edits (insertion, deletion, substitution) necessary to convert a given string into an exact match with the dictionary string (Levenshtein, 1965).

We utilize fuzzywuzzy (https://github.com/seatgeek/fuzzywuzzy, last access: 30 September 2021​​​​​​​) for this. fuzzywuzzy provides two methods to calculate a similarity score between two strings: ratio() or partial_ratio(). It also provides two functions to pre-process the strings: token_sort() and token_set(). In this work, we used the token_set_ratio() scorer to do fuzzy string matching to classify the Company_Litho or Comments entries as one of the Lithology Hierarchical Thesaurus entries (Table 1). token_set() pre-processes the strings by (1) splitting the string on white spaces (tokenization), (2) turning to lowercase, and (3) removing punctuation, non-alpha, non-numeric characters and unicode symbols. It tokenizes both strings (given string and dictionary string), splits the tokens into intersection and remainder, and then sorts and compares the strings. The sorted intersection component refers to the similar tokens between the two strings. Since the sorted intersection component (similar tokens between two strings) of token_set()​​​​​​​, will result in an exact match, the score will tend to increase when (1) the sorted intersection makes up a larger percentage of the full string and (2) the remainder components are more similar. The ratio() method then computes the standard Levenshtein distance between two strings. token_set_ratio() is found to be effective in addressing harmless misspelling and duplicated words but sensitive enough to calculate lower scores for longer strings (3–10 word labels), inconsistent word order, and missing or extra words. partial_ratio(), which takes the best partial of two strings or the best matching on the shorter substring, is not preferred as it does not address the difference and order in substring construction. token_sort() is not preferred as it alphabetically sorts the tokens that ignore word order and does not weight intersection tokens which do not address the behaviour of the strings in the logs.

Table 1Examples of fuzzy string matching output using different combinations of the fuzzywuzzy functions. The ticks and crosses beside the score indicate the preferred (ticks) result between the methods clustered together. The item in bold is the preferred method for this work.

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dh2loop calculates the token_set_ratio()​​​​​​​ between the Company_Litho or Comments (given string) and the entries in the Lithology Hierarchical Thesaurus (dictionary string). The tendency is to enumerate the descriptors before the rock name. For example, if the lithology in the logged interval is “basalt”, the free-text description could be something like “Dark grey to dark reddish brown, with olivine phenocrysts, largely altered andesitic basalt”. After processing the string, it will be left with “andesitic basalt”. To avoid misclassifying the rock as “andesite”, a bonus score is also added to add weight to the last word (in this case, “basalt”). Furthermore, the reader may worry that “basaltic andesite” will be simplified and classified as “andesite”. Since “basaltic andesite” is an established volcanic rock name, it will remain “basaltic andesite”. For the pair between Company_Litho or Comments and the entries in the Lithology Hierarchical Thesaurus with the highest score, the first synonym is stored as Detailed_Lithology. If the score is less than 80, it is classified as “unclassified rock”. The cut-off value is user-defined and can be chosen based on the performance of the matching on the subset of the desired region. If the performance is significantly lower, this indicates that the thesauri used in dh2loop may not be suitable to your area. The user may opt to update these thesauri to suit their needs. Once matched on Detailed_Lithology, the corresponding Lithology_Subgroup and Lithology_Group classifications are also fetched.

2.5 Fuzzy string matching assessment

The objective is to compare the Detailed_Lithology classification results obtained from two independent workflows: the (1) Lithology Code workflow and (2) Comments workflow. Using the Company_LithoCode, Company_Litho, Lithology Code workflow: Detailed_Lithology and Comments workflow: Detailed_Lithology from the dataset for the fuzzy string matching assessment, we can assess whether matches using the Comments workflow alone can sufficiently decode lithology.

To be able to assess the matching we take a look at the type of matches between Lithology Code workflow: Detailed_Lithology and Comments workflow: Detailed_Lithology. First, we define a match as retrieving an answer from the fuzzy string matching with a score greater than 80. It is important to note here that it only suggests that it succeeded in finding an answer above the score threshold but it does not necessarily mean that it is the correct answer. To further describe the quality of a match, we modified the following terms from the Simple Knowledge Organization System (Miles and Bechhofer, 2009) for this purpose:

  • a.

    “Exact match” suggests that both Lithology Code workflow and Comments workflow resulted in the same classification at all three levels. The match at the Detailed_Lithology level has an exact match, thus resulting in an exact match on the other two levels.

  • b.

    “Close match” suggests that the results at the Detailed_Lithology level are related rocks and belong to the same Lithology_Subgroup. This is usually caused by differing use of lithological nomenclature.

  • c.

    “Related match” suggests that the results at the Detailed_Lithology level are related rocks and belong to the same Lithology_Group.

  • d.

    “Broad match” refers to the Detailed_Lithology from Lithology Code workflow matches a Lithology_Subgroup in the Comments workflow.

  • e.

    “Narrow match” is the logical equivalent of a broad match. In this case, the Comments workflow resulted in a Detailed_Lithology level, while the Lithology Code workflow resulted in a Lithology_Subgroup level.

  • f.

    “Broader match” is similar to a broad match except that the Detailed_Lithology from Lithology Code workflow matches a Lithology_Group instead of a Lithology_Subgroup in the Comments workflow.

  • g.

    “Narrower match” is the logical equivalent of broader match. The Comments workflow results in a Detailed_Lithology while the Lithology Code workflow results in a Lithology_Group level.

  • h.

    “Failed match” suggests all levels of both workflows do not match. This is usually attributed to contrasting information from both fields or the algorithm fails. This category is an addition to the Simple Knowledge Organization System (SKOS) reference.

For better understanding of these relationships, examples are shown in Table 2 and Fig. 3.

Table 2Fuzzy string matching terminology used to describe the quality of matches based on the Simple Knowledge Organization System (SKOS) (Miles and Bechhofer, 2009). The values being compared are the Detailed_Lithology level for both the Lithology Code workflow and Comments workflow. The level at which the records are considered to match are in bold.

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https://gmd.copernicus.org/articles/14/6711/2021/gmd-14-6711-2021-f03

Figure 3SKOS graph showing the semantic, associative and hierarchical relationship in the Lithology Hierarchical Thesaurus. In this example, the terms “basalt” and “alkali basalt” are judged to be sufficiently the same to assert an exact match relationship (in green). “Basic volcanic rock” however is considered a close match (in cyan) and “gabbro” a related match (in blue). “Mafic fine-grained crystalline” and “mafic coarse-grained crystalline” are broader concepts and are thus considered a broad match (in orange) with “basalt” and “gabbro”, respectively. Broader match (in brown) is similar to broad matches but is used to refer a wider semantic difference between the two concepts. Narrow matches (in light purple) and narrower matches (in dark purple) are the logical equivalent of broad match and broader match. Failed matches is used to describe unrelated matches.

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The matching results can be visualized as confusion matrices, which are typically used in machine learning to compare the performance of an algorithm versus a known result. In this case, we are comparing the performance of the string matching using the Comments workflow against the results from the Lithology Code workflow. Each row of the matrix represents the matched lithology from the Comments workflow, while each column represents the matched lithology from the Lithology Code workflow. The diagonal elements represent the count for which the Comments workflow class is equal to the Lithology Code workflow. The off-diagonal elements are those that are misclassified by the Comments workflow. The higher the diagonal values of the confusion matrix the better, indicating many correct matches. The confusion matrices show normalization by class support size. This kind of normalization addresses the class imbalance and allows better visual interpretation of which class is being misclassified. The colour of the cell represents the normalized count of the records to address the uneven distribution of records across different classes. Relying on one metric to assess the matching can be misleading, therefore, we would like to use four metrics: accuracy, precision, recall and F1 score. It is worth mentioning that a small support influences the precision and recall. However, this is the nature of using real-world geological logs as more detail is given to particular lithologies or areas, depending on the interest of the study.

3 Case study: Yalgoo–Singleton greenstone belt

3.1 Study area

In this paper, we demonstrate the application of dh2loop to data from the Yalgoo–Singleton greenstone belt (YSGB) (Fig. 4), a geologically complex, largely heterogeneous and highly mineralized arcuate granite–greenstone terrane, in the western Youanmi Terrane, Yilgarn Craton, in Western Australia (Anand and Butt, 2010). The YSGB has good range of different lithologies in the area. Igneous rocks occur as extensive granitoid intrusions emplaced between 2700 and 2630 Ma (Myers, 1993), as well as ultramafic to mafic volcanic rocks formed as extensive submarine lavas and local eruptive centres of felsic and mafic volcanic rocks. Some layered gabbroic sills intruding the greenstone are also observed. Sedimentary rocks formed in broad basins during tectonic and volcanic quiescence consist of mostly banded iron formation (BIF) and felsic volcaniclastic rocks. The greenstone belt is metamorphosed to greenschist facies (Barley et al., 2008). The area is also covered by deeply weathered regolith which conceals mineral deposits hosted by the underlying bedrock. Regolith contains signatures of mineralization that are distal signatures of possible economically significant deposits (Cockbain, 2002). Furthermore, the YSGB is a major target for exploration as it has considerable resources of gold, nickel and bauxite as well as lesser amounts of a wide range of other commodities (Cockbain, 2002). It hosts multiple mineral deposits ranging from volcanogenic massive sulfide (Golden Grove, Gossan Hill) to orogenic gold (Mt. Magnet) to banded iron formations (Mount Gibson, Karara, Extension Hill). The geological and structural complexity, including its relevance to mineral exploration makes the YSGB a reasonable and sensible area to test the dh2loop thesauri, matching and upscaling.

https://gmd.copernicus.org/articles/14/6711/2021/gmd-14-6711-2021-f04

Figure 4The map shows the Yalgoo–Singleton greenstone belt highlighting the different mines and prospects in the area. The inset map shows the heterogeneous distribution and drill hole density from the legacy data available from the WAMEX database.

https://gmd.copernicus.org/articles/14/6711/2021/gmd-14-6711-2021-f05

Figure 5Extraction of lithology data for the YSGB. For the Lithology Code workflow, the extraction starts with filtering the dhgeology and dhgeologyattr table by the location extents and the Drill Hole Lithology Thesaurus. These records are matched with the entries from the Lithology Code Thesaurus. The Lithology Code workflow resulted in 235 606 records successfully matched in the fuzzy string matching. The Comments workflow extracts the records from the dhgeology and dhgeologyattr table as well, but this time using the Drill Hole Comments Thesaurus. In total, 47 823 records are present in both workflows, 7870 records of which are successfully matched. The 3074 unique entries from this are used as the dataset for the fuzzy string matching assessment.

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3.2 Lithology extraction: Lithology Code workflow and Comment workflow

Lithology extraction is divided into two workflows. For the Lithology Code workflow, the extraction starts with filtering the dhgeology and dhgeologyattr table by the location extents and the Drill Hole Lithology Thesaurus. The dhgeology table contained 47 062 drill holes across 115 companies with 797 975 lithology depth intervals with a corresponding 820 612 entries of lithology information in dhgeologyattr (Fig. 5). These records are matched with the entries from the Drill Hole Lithology Codes Thesaurus resulting in 273 684 matched records. The FromDepth and ToDepth for these records are then validated. In total, 74 records had equal FromDepth and ToDepth values. In total, 654 had values for FromDepth but null values for ToDepth. For both cases, ToDepth is calculated as FromDepth+ 0.01. The cut-off value of 80 is used for the string matching based on the performance of the matching in a subset of 1548 unique lithology codes from the Golden Grove area (Fig. 6). The Lithology Code workflow resulted in 273 684 intervals across 12 793 drill holes wherein 235 606 records are successfully matched in the fuzzy string matching. The remaining 546 819 entries did not obtain a match with a score greater than 80. An example of unmatched entries is provided in Table 2.

https://gmd.copernicus.org/articles/14/6711/2021/gmd-14-6711-2021-f06

Figure 6The user-defined cut-off score of 80 is chosen based on the results of the testing of different cut-offs on a smaller dataset within the YSGB area. As seen in this figure, the number of exact matches plateau at a score of 80.

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The Comments workflow extracts the records from the dhgeology and dhgeologyattr table as well, but this time using the Drill Hole Comments Thesaurus. For YSGB, the database has 262 567 records across 22 766 drill holes with free-text descriptions. In total, 47 823 records are present in both workflow. Since the free-text descriptions are extracted here to compare their results from fuzzy string matching, only 7870 records that also matched (both have a score greater than 80) in the Lithology Code workflow are retained.

3.3 Fuzzy string matching results

We present results from the data extraction using both workflows: Lithology Code and Comments. The dataset for the fuzzy string matching assessment consists only of the unique records matched on both Lithology Code workflow and Comments workflow (3074 records). It is visually checked from the records that the Lithology Code workflow: Detailed_Lithology results are sound classifications of the Company_Litho. This is done to make sure that these results could be regarded as the true value in the fuzzy string matching assessment. The overlaps between these two workflows suggest that the user may need to make choices to identify which is better suited for matching in their area of interest. To better understand the difference between these results, we looked at the matching overlaps between the two workflows (3074 entries). These matching overlaps are used to compare and describe the fuzzy string matching using the decoding the Company_LithoCode and using Comments.

We also take a look at the unique combinations of Company_LithoCode, Company_Litho, Lithology Code workflow: Detailed_Lithology and Comments workflow: Detailed_Lithology (53 unique records from the 3074 records). In total, 34 out of the 53 unique entries (64 %) result in matches between the Lithology Code workflow: Detailed_Lithology and Comments workflow: Detailed_Lithology. Of these, 26 are exact matches, 19 unique entries are close matches and 26 % percent are failed matches. The failed matches are due to unrelated descriptions in the Comments field which is used to obtain the results in Comments workflow: Detailed_Lithology. An example of this is the interval logged as “ironstone” (Company_Litho), but Comments contains “mafic schist”. Another less common reason is that Company_LithoCode is repeated in the Comments. An example of this is would be an interval logged as “colluvium” (Company_Litho) and the Comments as “COL”. The Comments workflow will result in “coal” instead.

  • Exact matches: of the total matched entries, 944 are exact matches (31 %) (Table 2). The exact matches are ideal outcomes as both workflows resulted in exactly the same answers.

  • Close matches: the close matches are common for coarse-grained igneous rocks, clastic sedimentary rocks, surficial residual rocks and filling structures. The coarse-grained igneous rocks such as gabbro, gabbroids and dolerites are used interchangeably in both fields. Comments can contain terms such as “gabbroic”, “granophyric gabbro to dolerite” or “intrusive granitoid to gabbro” resulting in close matches. Similar cases are observed between granodiorite and granite and between peridotite and coarse-grained ultramafic rocks. For clastic sedimentary rocks, the close matches are a result of gradation of grain size in the Comments. For example, an interval logged as mudstone (Company_Litho) is then described in Comments as “mudstone to sandstone” or “intercalated with siltstone”. Comments entries like this will result in “sandstone” and “siltstone”, respectively. Both are clastic sedimentary rocks but not an exact match to mudstone. Metasediments and quartz veins occur together, and what is described last dictates the Detailed_Lithology classification. Surficial rocks such as soil, duricrust, colluvium, laterite, calcrete, ferricrete and cover are used loosely or occur together, resulting in multiple combinations of these close matches.

  • Related matches: a total of 60 entries (3 %) resulted in related matches. For igneous rocks, this result is observed when Comments use rock type descriptors such as “komatiitic”, “basaltic” and “doleritic”. An example would be an interval logged as dolerite and then described in Comments as “doleritic basalt”. This would result in dolerite in the Lithology Code workflow and “basalt” in the Comments workflow. Both lithologies are igneous but have a different composition and textural implications. For sedimentary rocks, Lithology Code workflow results in sedimentary rocks classified based on grain size as they have been logged (“gravel”, “mud”). The Comments contains compositional descriptions such as “with silcrete” or “minor chert”. In this case, the Comments workflow will result in “silcrete” and “chert”. Both workflows will result in sedimentary rocks, but the Lithology Code workflow will result in “clastic” rocks while the Comments workflow will classify these to “siliceous” at the Lithology_Subgroup level. The related matches for structures occur across coincident lithologies such as “mylonite”, “vein”, “fault” and “breccia”, which could either be “fillings” or “fault_rock” in the Lithology_Subgroup.

  • Broad and narrow matches: no broad matches are noted and only one narrow match is obtained (Table 3). The interval is logged as “ironstone” with “BIF” in Comments, “ironstone” being a more general description for “banded iron formation”.

  • Broader and narrower matches: more common cases are broader and narrower matches, indicating that there is a bigger relationship gap between the data in Company_Litho and Comments. Broad matches are a result of low-detail free-text descriptions in Comments. For example, an interval logged as “gabbro” is described as “medium-grained mafic”, “massive mafic” or “rich mafic”. The inverse is noted for narrower matches; the interval is logged as “sediment”, but in Comments the interval is described as “siliceous sediments”.

  • Failed matches: a total of 1694 entries resulted in failed matches (55 %). Failed matches occur when Company_Litho and Comments contain different information. This could be because the Company_Litho contains the main lithology while Comments contains all other lithologies intercalated in the interval. Another reason is that Company_Litho is re-logged based on adjacent intervals without amending Comments. “Mudstone” had failed matches with a wide range of lithologies, such as “amphibolite”, “dolerite”, “saprolite”, “duricrust”, “laterite”, “banded iron formation”, “chert”, “phyllite”, “schist” and “vein”. The same is observed for igneous rocks such as “coarse-grained ultramafic rock”. For “chert”, the failed matches are within a range of sedimentary rocks: “alluvium” and “mud”, “amphibolite” and “massive sulfide”, “carbonate”, “vein” and “pegmatite”.

Table 3Distribution of matches across the fuzzy string matching dataset. A total of 45 % of the unique records are matched reasonably, 31 % of which are exact matches, 6 % close matches, 3 % related matches, 3 % Broader matches and 3 % narrower matches.

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The matching results are visualized as confusion matrices, comparing the performance of the string matching using the Comments workflow against the results from the Lithology Code workflow. From the 3074 unique records, we use a total of 1200 samples for the confusion matrices. The reason for this difference is the limitation of building a confusion matrix wherein both workflows look at the same classes and ensuring that both workflows produce a match.

3.3.1 Structure and texture

While geological structures are not lithologies, they are sometimes described in lithological logs (Fig. 7). Structures common in the YSGB area are faults and veins. Figure 7 shows the confusion matrix for the structures and textures. The vertical axis represents the matches from the Lithology Code workflow while the horizontal axis for the results from the Comments workflow. We consider a dataset of 52 unique records where we are trying to assess whether the Comments workflow results in the same classification as the Lithology Code workflow. Figure 7 shows that there are 6 records classified as “fault” and 46 records as “vein”. When looking at the classification of “faults” we can say that there are two records that are true positives. In total, 46 records are true negative pairs, as in this 2 × 2 matrix, if it is not a “fault”, it is a “vein”. True negatives together with true positives are the exact matches and suggests that the Comments workflow identified it correctly. To have a better look at the parts that are not classified correctly we look at the false positives and false negatives. False positives represent the number of records classified as “fault” but based on the Lithology Code workflow are not. In this case, there are no false positive values. False negatives represent number of records classified as “vein” but are actually “faults” based on the Lithology Code workflow.

https://gmd.copernicus.org/articles/14/6711/2021/gmd-14-6711-2021-f07

Figure 7Confusion matrix for structure and texture comparing the fuzzy string matching results from the Lithology Code workflow (vertical axis) and Comments workflow (horizontal axis). The heatmap shows the values normalized to the support size to address the imbalance between classes. The values shown in the cells indicate the number of samples classified for the class. Empty cells indicate zero samples. The structures and texture Lithology_Group had an accuracy of 92.3 % across 52 samples: 46 for veins and 6 for faults.

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A total of 48 exact matches are noted, 46 records of which are “veins” and 2 records are “faults”. This can be surmised by looking into the diagonal cells. The rest of the “veins” (4 records) are related matches as “faults”. They are considered related matches as faults and veins tend to coexist in nature. In addition, faults often occur as fault zones, with infill clay or silica vein sulfides which are described in Comments that then obscures the classification. These structure-related lithological descriptions can be used as proxies in further geological studies.

3.3.2 Igneous rocks

The confusion matrix for igneous rocks considers a dataset of 218 unique records (Fig. 8). Dealing with a larger matrix is not as straight-forward as the previous matrix. When looking at the classification of a single lithology, the true positives are where both axes refer to the same class. For example, for “basalt” there are 15 records of true positives which correspond to the exact matches. The false positives are the sum of all the other entries along the corresponding vertical axis, and the false negatives are the sum of all the entries along the corresponding horizontal axis. The sum of all the other cells represent the true negatives. For “basalt”, there are 15 true positives, 13 false positives, 15 false negatives and 175 true negatives. This results in 54 % classification precision for “basalt”.

https://gmd.copernicus.org/articles/14/6711/2021/gmd-14-6711-2021-f08

Figure 8Confusion matrix for igneous rocks comparing the fuzzy string matching results from the Lithology_Code workflow (vertical axis) and Comments workflow (horizontal axis). The heatmap shows the values normalized to the support size to address the imbalance between classes. The values shown in the cells indicate the number of samples classified for the class. Empty cells indicate zero samples.

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This statistic is helpful in quantifying the performance of the classification. However, what it does not capture is the semantic and hierarchical relationship of the false negative pairs. As shown in Figs. 8, 3 records are classified as “komatiite” and 12 records are classified as “mafic”. The “komatiite” matches are a result of when Comments describe the basalts as “komatiitic basalts”. This can be regarded as a related match. The 12 records which are classified as “mafic” are considered a “broader match”. For the false positive values, the “mafic” records are narrower matches while the “dolerite” is a related match. These quantitative assessments of the matches show us that although the matching is not perfect, the context of the misclassification is not severe.

“Dolerite” is the most common igneous rock matched. This could be attributed to the sampling bias towards dolerite as it is often targeted by drilling as it is used as targeting criteria for gold mineralization (Groves et al., 2000). Given that dolerites can be described by their mafic component or be confused as gabbro when weathered, the descriptions contain the strings “mafic” and “gabbro” which explain close and broader matches. Gabbros are also common in the YSGB. Some of the “gabbros” are classified as “mafic” in the Comments Detailed_Lithology. This is another example of a broader match. However, it is important to note that although it is not an exact match, a broader match can be useful in geological studies relating to rock composition as gabbros are members of mafic rocks. In total, 40 % of the igneous rock that are mismatched at the Detailed_Lithology level are broader matches (matches correctly at Lithology_Group).

3.3.3 Sedimentary rocks

The largest Lithology_Group of the lithological entries relates to sedimentary rocks (800 entries) (Fig. 9). In total, 457 of the 800 entries are true positive classification of mudstones. Mudstones are common as shale beds. Mudstones resulted in related matches with “chert” and “ironstone”. The misclassification occurs when the logs describe intervals wherein the mudstone occurs together and is intercalated with these lithologies. A few mudstones (17) are matched as sandstone due to textural and grain size descriptors (close match). In total, 48 % of the cherts resulted in exact matches. In total, 39 records of cherts resulted in failed matches as their Detailed_Lithology level matched with “banded iron formation”; it occurs when intercalated, such as “cherts with BIF”, or includes string descriptors, such as “BIF-fy”.

https://gmd.copernicus.org/articles/14/6711/2021/gmd-14-6711-2021-f09

Figure 9Confusion matrix for sedimentary rocks comparing the fuzzy string matching results from the Lithology Code workflow (vertical axis) and Comments workflow (horizontal axis). The heatmap shows the values normalized to the support size to address the imbalance between classes. The values shown in the cells indicate the number of samples classified for the class. Empty cells indicate zero samples.

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3.3.4 Metamorphic rocks

Out of a total of 61 metamorphic rock entries, 60 are matched correctly (Fig. 10). Most of these are “schists” as the YSGB area is rich in talc–carbonate schists. The Company_Litho entry “amphibolite mica schist”, which is matched as “amphibolite”, matches as “schist” in the Comments workflow. This is considered a related match.

https://gmd.copernicus.org/articles/14/6711/2021/gmd-14-6711-2021-f10

Figure 10Confusion matrix for metamorphic rocks comparing the fuzzy string matching results from the Lithology Code workflow (vertical axis) and Comments workflow (horizontal axis). The heatmap shows the values normalized to the support size to address the imbalance between classes. The values shown in the cells indicate the number of samples classified for the class. Empty cells indicate zero samples.

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3.3.5 Surficial rocks

Fuzzy string matching accuracy of surficial rocks scored 45 % on a total of 69 entries (Fig. 11). Saprolites are matched as saprolite (exact match), rock (failed match) and saprock (close match). In instances where saprock is inputted as “sap rock”, it results in a failed match as “rock”. “Soil” is commonly used in logs to refer to the first intercept of highly weathered, clay-rich and unidentifiable intercept. “Soil” is classified with the highest variability of terms: “soil” (exact match), “rock” (failed match), “duricrust” (close match), “colluvium” (related match) and “calcrete” (close match). “Laterite” is matched to “colluvium” (related match), “duricrust” (close match) and “lag” (close match). “Lag” generally matches with “colluvium” (related match). However, when described in Comments, it can be associated with its protolith which results in a failed match as “rock”.

https://gmd.copernicus.org/articles/14/6711/2021/gmd-14-6711-2021-f11

Figure 11Confusion matrix for surficial rocks comparing the fuzzy string matching results from the Lithology Code workflow (vertical axis) and Comments workflow (horizontal axis). The heatmap shows the values normalized to the support size to address the imbalance between classes. The values shown in the cells indicate the number of samples classified for the class. Empty cells indicate zero samples.

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4 Discussion

4.1dh2loop functions and notebooks

The dh2loop library supports a workflow that extracts, processes and classifies lithological logs (Appendix A4). This library is built to extract drill hole logs from the WAMEX database. The assumptions made in the entire workflow attempt to replicate the thought process of a geologist performing the data extraction, data quality checks and lithological log classification manually. However, it can be adapted for other geological relational databases or from other table formats. An example using comma-separated values tables (CSVs) is shown in the notebook Exporting and Text Parsing of Drillhole Data Demo.

In addition to the data extraction, downhole de-surveying and lithological matching functions discussed, dh2loop also provides functionalities and a notebook demonstrating harmonization of drill hole data. This is useful for combining and correlating drill hole exports of different properties such as lithology, assays and alteration. It is also possible to export this information in Visualization Toolkit format (.VTK). It also provides a notebook that demonstrates the application of lasio and striplog on dh2loop interval table exports. WAMEX reports can also be interactively downloaded through a notebook provided in the package.

4.2 Thesauri

dh2loop provides the user with nine thesauri that deal with the extraction of collar, survey and lithology interval tables. For the extraction of other properties, such as downhole alteration, geochemistry, mineralogy and structures, at least one thesaurus is needed for each attribute we would like to export. These thesauri are built manually by inspecting all the terminologies available in the database. Although creating them can be tedious, updating an existing thesaurus is as simple as adding and/or removing a word for the list. There are many other properties available in the database that could be exploited using the existing methodology; thus there is an incentive in finding a way to improve the methodology of building these thesauri. Analysis on the syntax of the existing thesauri may help in automating the creation of other thesauri.

The Hierarchical Lithology Thesaurus puts equal weight on each of the entries in the thesaurus. By knowing the geology in a user's area, the matching can be improved by adding more weight to prevalent lithologies through adding a bonus score.

4.3 Data extraction

dh2loop supports the data extraction of collar, survey and lithology interval tables. The main consideration in the data extraction is that the data retrieved are complete, relevant and useful. We would rather throw erroneous or questionable data out and have the rest with a high level of confidence than the other way around. The lithology extraction using the Lithology Code workflow shows that the bottle neck to its extraction rate is the extensiveness of the Drill Hole Lithology Codes Thesaurus. Since the thesaurus did not have information for all companies in the area, only 34 % of the available information is retrieved. The extraction results for the Comments workflow cannot be compared with the Lithology Code workflow as only the intersection of both workflows is considered in this study.

4.4 Assessment of string matching results

The number of successful matches are dependent on the selected cut-off score. The selection of a cut-off score is a balance between the number of matched records and the exact match percentage. In this case study, we selected a cut-off score of 80 since this is where the number of exact matches plateaus (Fig. 6). A lower cut-off score could be used, depending on the familiarity with the data and/or the purpose of the drill hole processing. For our case, we wanted to be as conservative as possible without being too stringent (cut-off score 100).

The string matching results highlight that geological drill core logging is prone to human error and bias and results in incorrect logs. Sometimes even if the data are available and correct, they are not in a format that can be directly extracted. For example, Comments are filled with a string description such as “same as above” and “-do-“. Currently, for this case, dh2loop returns without a match, as replacing “same as above” requires building a dictionary for all possible permutations to refer to this. This is not included in the scope of this work. In the future, we could be able to search through the previous entries to retrieve the correct lithology. Furthermore, the code does not handle and check for inconsistencies in the logs. It only addresses the inconsistencies in nomenclature and not the logging itself. The string matching misclassification results illustrate the importance in the consistency and level of detail being put into logging and identify differences in convention or uncoordinated logging among geologists. dh2loop provides a notebook that demonstrates using striplog to improve the consistency of the logs through data pruning and annealing. In the future, the geochemical compositions can be used to counter check any lithology assigned to the interval.

Comparing the string matching between the Lithology Code workflow and Comments workflow, the Lithology code workflow results in a higher matching rate; 86 % of the extracted data is successfully matched. Comparing this subset to the Comments workflow, the matching rate is much lower at 16 %. This shows that the Lithology Code workflow, while potentially tedious, results in a higher percentage of successful matches. However, if we are considering a regional study involving multiple companies and drilling campaigns, building thesauri can be time-consuming depending on the size of the region being studied, the number of attributes of interest, and the number of companies and drilling campaigns. This could range from a couple of hours to months. It can also be tedious as it involves inputting errors and inconsistencies as well as exhausting all permutations for decision-tree-based logging systems. The thesauri provided by dh2loop could serve as a starting point to automate this process using recent advances in NLP and machine learning.

String matching using Comments provides a quicker way to standardize and classify rocks. The comprehensive Clean-up Dictionary assists in improving the matching accuracy. Given the context that we are dealing with, i.e. legacy data, an extraction rate of 16 % is a low extraction rate, but there is value in being able to obtain 7870 records more than what was previously deemed “unusable“. With minimal effort, we obtain additional geological data, which although it has a smaller percentage (31 % of exact matches), provides reasonably high confidence in its quality. It is important to note that most of the time failed matches are not a result of the limitations of the algorithm but of the legacy geological logs themselves. Inconsistent logs (Company_Litho data are different from Comments) usually occur in the following cases.

  1. The logs are post-processed and correlated with the rest of the hole or neighbouring drill holes and changes are made to the Company_Litho but none to the Comments field.

  2. The Comments have a higher level of detail than the Company_Litho. In this case, we may get a lithology at Lithology_Subgroup from the Lithology Code workflow and a Detailed_Lithology from the Comments workflow.

  3. The Company_Litho have a higher level of detail than the Comments.

  4. The Comments contain the description of the whole intercept, which could include a contact of two lithologies or intercalating lithologies.

From the results of the confusion matrix (Sect. 3.3), some rock groups are more sensitive to these inconsistencies than others. There is higher confidence in the classification of structures and textures and metamorphic rocks in the study area dataset, but not necessarily in others. There could be metamorphically dominated terranes where the subordinate igneous rocks will be classified with higher confidence. The user should be more careful when dealing with sedimentary and surficial rocks. They are more difficult to classify as the way they are described is highly variable between different geologists. For structure-related lithological descriptions the small number of misclassifications occurs where faults, veins and fillings coexist. For metamorphic rocks, entries like “mica amphibolite schist” can cause broader matches with the confusion of whether to classify it as “amphibolite” or “schist”. “Schist” is a textural term for medium-grade metamorphic rock with a medium- to coarse-grained foliation defined by micas, while “amphibolite” is a compositional term representing a granular metamorphic rock which mainly consists of hornblende and plagioclase. One should be wary about these possibilities as they may impact the interpretation of the geology in the area. For sedimentary rocks, descriptions of intercalated lithologies or the presence of major and minor lithology can result in failed matches. The lack of a standard syntax as to how free-text descriptions are recorded impacts the classification. This procedure provides a basis for creating a pre-standard, not so much providing a guide of practice but highlighting what should not be done and what practices create ambiguity. Standardization will definitely reduce subjectivity, and it is for the geological surveys to decide and implement. It is also important to note that a “standard” would be tricky to achieve as the information and level of detail contained in logs is highly dependent on the purpose of the study. Igneous rocks perform fairly well; most of what is not captured as exact matches is captured at least as broader matches. These are usually related to either an inconsistent level of detail between the fields or rock types used as descriptors (“komatiitic”, “andesitic”, basaltic”).

Low matching accuracy in surficial rocks can be attributed to the lack of universally agreed terminology for deeply weathered regolith, poorly defined and misapplied surficial rock nomenclature, a wide range and variation in materials within the regolith, and difficulty in bulk mineral identification from macroscopic samples. Furthermore, since the degree of weathering of minerals generally increases from the bottom to the top of in situ weathering profiles, the intermixing of strongly weathered and less weathered grains may cause confusion (Cockbain, 2002). Ubiquitous, highly variable and less interesting lithologies also cause mismatches. An example of this is “soil”. Soils are technically are not rocks, but the term is commonly used in logs to refer to the first intercept of the regolith or to describe highly weathered, clay-rich and unidentifiable intercept. Soils vary in character from thin, coarse-grained, poorly differentiated lithosols to thick, well-differentiated silt and clay-rich soils. Soils are classified with the highest variability of terms: “soil”, “rock”, “duricrust”, “colluvium” and “calcrete”. There are also certain lithologies with ambiguous nomenclature conventions, like “laterite”, “duricrust”, “lag”. Some geologists use laterite to refer to the whole lateritic profile (ferruginous zone, mottled zone and saprolite), while others use it to refer to the ferruginous zone (Eggleton, 2001). Iron crust, duricrust, lateritic gravels and lag are commonly used interchangeably. Duricrust and iron crust are terms to describe ferruginous indurated accumulations at or just below the surface. The difference in usage of the term laterite and the interchangeability of duricrust and lag explains the misclassification of “laterite” as “colluvium”, “duricrust” and “lag”. Another example is “saprolite” and “saprock”. They are ambiguous terms as they both represent the lower horizons of lateritic weathering profiles, with saprolites having more than 20 % of weatherable minerals altered and saprock having less than 20 % of the weatherable minerals being altered (Eggleton, 2001). This arbitrary limit makes the terminology used in the logs easily interchangeable, thus affecting the Detailed_Lithology matching.

Ideally, a combination of the Lithology Code workflow and the Comments workflow should result in a more robust classification. This will also allow the user to have a better look at the result of both workflows and decide what is appropriate for one's purpose.

4.5 Value of the lithological information extracted for multiscale analyses

The dh2loop lithology export provides a standardized lithological log across different drilling campaigns. This information can be readily imported into 3D visualization and modelling software. This allows for drill hole data to be incorporated into 3D modelling, providing better subsurface constraints, especially at a regional scale. It also allows the user to decide on the lithological resolution necessary for their purpose. It provides a three-level hierarchical scheme: Detailed_Lithology, Lithology_Subgroup and Lithology_Group. This can be used as an input to multiscale geological modelling. dh2loop can be improved by correlating these lithologies to their corresponding stratigraphic formations. With the spatial extents of the different geological formations and their lithological assemblages (GSWA Explanatory Notes System) as well stratigraphic drill holes, it may be possible to infer the corresponding stratigraphic formation.

5 Conclusions

The dh2loop library is an open-source library that extracts geological information from a legacy drill hole database. This workflow has the following advantages:

  1. It maximizes the amount of legacy geoscientific data available for analysis and modelling.

  2. It provides better subsurface characterization and critical inputs to 3D geological modelling.

  3. It standardizes geological logs across different drilling campaigns, a necessary but typically time-consuming and error-prone activity.

  4. It provides a set of complementary thesauri that are easily updated and are individually useful references.

  5. It implements a hierarchical classification scheme that can be used as an input to multiscale geological modelling.

  6. Classification results can also be used as a tool to improve future geological logging works by revealing common errors and sources of inconsistencies.

Appendix A:dh2loop package information

A1 Conventions and terminologies

Table A1List of conventions and terminologies used across the paper. Links to the thesauri are also indicated.​​​​​​​

* last access: 30 September 2021.

Download XLSX

A2 Installation and dependencies

Installing dh2loop can be done by cloning the GitHub repository with $ git clone https://github.com/Loop3D/dh2loop.git (last access: 30 September 2021)​​​​​​​ and then manually installing it by running the Python setup script in the repository: $ Python setup.py install.

It primarily depends on a number of external open-source libraries:

  1. fuzzywuzzy (https://github.com/seatgeek/fuzzywuzzy), which uses fuzzy logic for string matching (Cohen, 2011)

  2. pandas (https://pandas.pydata.org/, last access: 30 September 2021​​​​​​​) for data analysis and manipulation (McKinney, 2011)

  3. psycopg2 (https://pypi.org/project/psycopg2/, last access: 30 September 2021), a PostgreSQL database adapter for Python (Gregorio and Varrazzo, 2018)

  4. numpy (https://github.com/numpy/numpy, last access: 30 September 2021)

  5. nltk (https://github.com/nltk/nltk, last access: 30 September 2021), the Natural Language Toolkit, a suite of open-source Python modules, datasets, and tutorials supporting research and development in natural language processing (Loper and Bird, 2002).

  6. pyproj (https://github.com/pyproj4/pyproj, last access: 30 September 2021), Python interface to PROJ (cartographic projections and coordinate transformations library).

Code describing basic drill hole operations, such as de-surveying (process of translating collar (location) and survey data (azimuth, inclination, length) of drill holes into XYZ coordinates in order to define its 3D geometry of the non-vertical borehole), is heavily inspired by the pyGSLIB drill hole module (Martínez-Vargas, 2016). The pyGSLIB drill hole module is re-written into Python to make it more compact with less dependencies and to tailor it to the data extraction output.

A3 Documentation

dh2loop's documentation provides a general overview over the library and multiple in-depth tutorials. The tutorials are provided as Jupyter Notebooks, which will provide the convenient combination of documentation and executable script blocks in one document. The notebooks are part of the repository and located in the notebooks folder. See http://jupyter.org/ (last access: 30 September 2021)​​​​​​​ for more information on installing and running Jupyter Notebooks.

A4 Jupyter notebooks

Jupyter notebooks are provided as part of the online documentation. These notebooks can be executed in a local Python environment (if the required dependencies are correctly installed). In addition, static versions of the notebooks can currently be inspected directly on the github repository web page or through the use of nbviewer.

  1. WAMEX Interactive report downloads (https://github.com/Loop3D/dh2loop/blob/master/notebooks/0_WAMEX_Downloads_Interactive.ipynb, last access: 30 September 2021​​​​​​​)

  2. Exporting and Text Parsing of Drillhole Data From PostgreSQL database (https://github.com/Loop3D/dh2loop/blob/master/notebooks/1_Exporting_and_Text_Parsing_of_Drillhole_Data_From_PostgreSQL.ipynb, last access: 30 September 2021)

  3. Exporting and Text Parsing of Drillhole Data Demo (https://github.com/Loop3D/dh2loop/blob/master/notebooks/2_Exporting_and_Text_Parsing_of_Drillhole_Data_Demo.ipynb, last access: 30 September 2021)

  4. Harmonizing Drillhole data (https://github.com/Loop3D/dh2loop/blob/master/notebooks/3_Harmonizing_Drillhole_Data.ipynb, last access: 30 September 2021).

Appendix B: Collar and survey data extraction

B1 Collar extraction

The collar extraction workflow (Fig. B3) fetches the CollarID, HoleID, Longitude and Latitude information from the collar table (Fig. B3a, red), while the corresponding RL and MaxDepth values are fetched from the collarattr table using the Drill Hole Collar Elevation Thesaurus (Fig. B3b, blue) and Drill Hole Maximum Depth Thesaurus (Fig. B3c, orange). With the minimum input of a region of interest, the dh2loop library exports a comma-separated values file (CSV) listing the drill holes in the area with the following information:

  1. CollarID: the CollarID for a drill hole is identical in all tables in order for data to be associated with that drill hole.

  2. HoleID: this is the drill hole name, as the company would internally identify the drill hole.

  3. Longitude and Latitude: both values are expressed in WGS 1984 lat/long (EPSG:4326).

  4. Relative level (RL): we use RL here to refer to elevations of survey points with reference to the mean sea level. This definition of RL is equivalent to the elevation values used in digital elevation models (DEMs). This value is extracted by using the Drill Hole Collar Elevation Thesaurus to filter the values referring to relative level. More than one value can be fetched due to duplicate company submissions or multiple elevation measurements, in which case the code retains the value with most decimal places assuming that higher precision corresponds to better accuracy. If no elevation values are fetched from the database the entire record is skipped. Non-numeric values are also ignored.

  5. Maximum depth (MaxDepth): this value is extracted by using the Drill Hole Maximum Depth Thesaurus. Due to duplicate company submissions, there can be more than one value fetched. Since there is no submission date information, the code takes the value with the largest value assuming it is the latest submission.

  6. Calculated X, Y values of projected coordinates: these values are commonly calculated and used to be able to plot the drill hole in a metric system to be able to accurately display and measure distance within and between drill holes. The projection system used in the calculation is based on the input specified in the configuration file.

The extraction of the collar data for YSGB resulted in a collar file with 68 729 drill holes. This information is extracted from the collar table with 73 881 drill holes with 769 981 rows of information from collarattr. It includes the location of the collar both in geographic and projected coordinated systems, relative level (RL) and maximum depth (MaxDepth). A total of 136 100 records for RL is retrieved from the database, 1526 of which are disregarded: 846 records for having an RL value greater than 10 000 m and 680 non-numeric records. These discarded values are retrieved from the attribute column “RL_Local”. In spite of it being an isolated issue for “RL_Local”, the attribute column is retained as it retrieves sensible values for other companies. The discarded values are limited to data from two companies (4085, 4670) for RL attribute columns “TD” and “DEPTH”. A total of 58 706 records for MaxDepth are retrieved from the database, 58 642 of which are extracted as is, while 64 entries are disregarded for having a value of −999. The discarded values come from eight companies. Null values are disregarded and absent RL or MaxDepth values. The “clean” collar export file contains at least either a value for RL or MaxDepth. The reasoning behind keeping records with at least one of the two fields is that there are other ways to extract RL or MaxDepth from the database. RL values can be extracted from digital terrain models and MaxDepth values can be taken for the largest ToDepth values from the other tables. In total 93 % of the available collar data in the area is extracted successfully. This can be improved by implementing alternative ways of retrieving RL and MaxDepth values. For example, if no RL values are fetched from the database, they could be fetched from open-source digital terrain models (DTMs) or the SRTM (Shuttle Radar Topography Mission). As for missing MaxDepth values, the maximum ToDepth values in the survey or interval tables could be used.

B2 Survey extraction

The survey extraction workflow (Fig. B4) fetches the DHSurveyID, CollarID and Depth information from the dhsurvey table (Fig. B4a, red), while the corresponding azimuth and inclination values are fetched from the dhsurveyattr table using the Drill Hole Survey Azimuth Thesaurus (Fig. B4b, blue) and Drill Hole Survey Inclination Thesaurus (Fig. B4c, orange).With the same inputs defined in the configuration file, the dh2loop library outputs a survey CSV file containing the following information: CollarID, Depth, Azimuth, Inclination and Calculated X, Y, Z values. The workflow accommodates underground holes drilled upwards as long as the metadata and data appropriately describe them as such. For all properties, all non-numeric values are ignored. For Depth, negative values are replaced by their absolute value. This assumption is made as some drill holes have negative depth information and it is technically not possible to have a negative length. This is done by some companies to denote that the depth measure is going upwards (usually for underground probing drill holes) rather than downwards. For Azimuth, the code fetches values between 0–360, thus ignoring values greater than 360. Values between −360 to 0 are assumed to be anticlockwise from the north. If there is no survey information for a drill hole present in collar, the Azimuth value is set to 0. The X, Y, Z, values are calculated using the minimum curvature basing the code on the pyGSLIB drill hole module.

For the survey extraction, the dhsurvey table contained 146 713 survey depth intervals (from 45 708 drill holes) with a corresponding 850 507 entries of supplementary survey information in dhsurveyattr. Survey extraction in YSGB resulted in 126 669 pieces of survey depth information across 45 708 drill holes with azimuth (−52.5 to 359) and inclination measurements (0–90) for each depth interval. A total of 517 592 records for Azimuth are retrieved from the database. In total, 77 Azimuth values greater than 360 are retrieved and thus disregarded. In total, 152 values are non-numeric values and are also disregarded. These discarded values involved 228 holes across 10 companies. A value of 0 is assigned to missing Azimuth values. A total of 118 223 records for Inclination are fetched from the database, 118 138 of which are extracted as is, while 95 entries are disregarded for having a value greater than 90. A values of −90 is assigned as the default for inclination. The discarded values correspond to 94 drill holes across five companies. The survey extraction rate of 86 % is fairly good. dh2loop ensures that the Azimuth and Inclination values are sensible measurements before including them in the extracted output file. An improvement that could be implemented is to run an assessment on the deflection angles for each drill hole and flag intervals with unrealistic deflection angles.

https://gmd.copernicus.org/articles/14/6711/2021/gmd-14-6711-2021-f12

Figure B1Simplified example of a drill hole (1.A) and its corresponding interval tables collar (1.B), survey (1.C) and lithology (1.D). The black circle denotes the collar location of the drill hole which is obtained from a collar table (1.B). The purple line represents the first downhole interval taking its deviation data from the survey table (1.C) and the lithology information from the lithology table (1.D). The same applies for the second interval (orange line) and the third interval (blue line). The orange line follows the same trajectory as the first interval as it uses the same entry in the survey table (1.C). The blue line has no lithology data as this information is not present in the lithology table (1.D). The MaxDepth denotes the total drill length (1.B).

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https://gmd.copernicus.org/articles/14/6711/2021/gmd-14-6711-2021-f13

Figure B2Simplified WAMEX database schema showing the one-to-many relationship between the collar table and the collarattr table (red solid line). collarattr stores other attributes that describe each unique drill hole, such as maximum depth and elevation. The figure also shows the relationship between the collar table and the other interval tables such as dhsurvey, dhsurveyattr, dhgeology and dhgeologyattr. The deviation of the drill hole is stored in a table, dhsurvey, with a primary key (DHSurveyID) that refers to each unique depth of a drill hole. This primary key has a many-to-one relationship with collar, as there are multiple depth measurements for each drill hole. Furthermore, dhsurvey also has a one-to-many relationship with the table dhsurveyattr, which stores additional attribute information regarding survey, such as Azimuth and Inclination readings. The example shows the relationship between tables for the first (red dashed line) and second interval (red dashed–dot line). Each drill hole in the WAMEX database is identified by its geographic coordinates and a unique ID (CollarID) in the collar table. The drill hole 3D geometry is described in the survey tables (dhsurvey, dhsurveyattr). This similar relationship is maintained with interval tables, except that the primary key (e.g. DHGeologyID) is used to refer a unique downhole interval rather than a depth measurement. For lithological information, we refer to tables dhgeology and dhgeologyattr. dhgeologyattr contains information such as rock names and free-text descriptions, while dhgeology provides information on which hole and interval depth those data refer to. This information can be joined and extracted through SQL (Structured Query Language) queries.

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https://gmd.copernicus.org/articles/14/6711/2021/gmd-14-6711-2021-f14

Figure B3Collar extraction workflow.

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https://gmd.copernicus.org/articles/14/6711/2021/gmd-14-6711-2021-f15

Figure B4Survey extraction workflow.

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Code and data availability

dh2loop is a free, open-source Python library licensed under the MIT License. It is hosted on the GitHub repository (https://github.com/Loop3D/dh2loop) and can be cited as http://doi.org/10.5281/zenodo.4043568 (Joshi et al., 2020).

Author contributions

MJ contributed the original idea, which led to further developed by RJ. KM developed the code. MJ, ML and GP provided guidance and direction in the research. RJ prepared the paper with contributions from all co-authors. Lastly, MJ supervised the entire process.

Competing interests

The authors declare that they have no conflict of interest.

Disclaimer

Publisher’s note: Copernicus Publications remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Acknowledgements

The research was carried out while the first author was in receipt of a Scholarship for International Research Fees (Australian Government Research Training Program Scholarship) and an Automated 3D Geology Modelling PhD Scholarship (University Postgraduate Award) at the University of Western Australia. We acknowledge the support from the ARC-funded Loop: Enabling Stochastic 3D Geological Modelling consortia (LP170100985) and DECRA (DE190100431). The work has been supported by the Mineral Exploration Cooperative Research Centre, whose activities are funded by the Australian Government's Cooperative Research Centre Program. This is MinEx CRC Document 2021/49. We would also like to acknowledge Tim Ivanic for his input on the geology of the Yalgoo–Singleton greenstone belt.

Financial support

This research has been supported by the Australian Research Council (grant nos. LP170100985 and DE190100431).

Review statement

This paper was edited by Andrew Wickert and reviewed by Matt Hall, Ignacio Fuentes, and one anonymous referee.

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